title: GBM39, ec, GRO-seq, rep2

description:
GBM39ec_GRO_rep2
GRO-seq

data_processing:
*library strategy: GRO-seq
Paired end reads were mapped to human reference genome (hg38) and gencode v42 using STAR, version 2.7.10b17, with --runMode alignReads
Reads with MAPQ values less than 10 were filtered using samtools 1.8
PCR duplicates are removed with Picard MarkDuplicates
Bigwig (.bw) files were generated for each strand using bamCoverage (py-deeptools/3.3.1_py36) with -binSize 10 --normalizeUsing CPM
HOMER (v4.11.1) was used for de novo transcript identification on each strand separately using the default GRO-seq settings
Assembly: hg38
Supplementary files format and content: Bigwig (.bw) files contain normalized GRO-seq signal separated by DNA strands for visualization.

molecule: nuclear RNA

growth_protocol: COLO320: RPMI, 10% FBS, 1% pen/strep; GBM39: DMEM/F12, 1x B27, 20ng/ml EGF, 20ng/ml FGF, 1mg/ml heparin, 1% pen/strep

extract_protocol:
Purified nuclei were incubated with equal volume of nuclear run on master mix (10mM Tris-HCl pH 8.0, 5mM MgCl2, 1mM DTT, 300mM KCl, 0.5mM ATP, 0.5mM GTP, 0.003mM CTP (unlabeled rNTPs from Roche 11277057001), 0.5mM Bromo-UTP (Sigma B7166), 1% Na-laurylsarcosine, 1ul RNase inhibitor/100ul) and incubated for 5 minutes at 30C. COLO320 samples were then treated with DNAse for 30min, then proteinase K for 1hr, followed by RNA extraction. GBM39 cells were mixed thoroughly with Trizol LS, then chloroform was added and RNA was extracted. Purified RNA from all cell lines was hydrolyzed in 0.2N NaOH for 10min then neutralized with 500mM Tris-HCl pH 6.8. Samples were then treated with T4 PNK (90-120min) and then mRNA decapping enzyme (30min). EDTA was then added to a final concentration of 25mM and samples were heated to 75C. Samples were then added to anti-BrdU agarose beads that had been blocked in 0.1% polyvinulpyrrolidone and 1ug/ml ultrapure BSA) and incubated with rotation for one hour a room temperature. Beads were washed in a series of wash buffers and then eluted at 42C. Eluted RNA was then purified by phenochloroform extraction (COLO320) or RNA cleanup kit (GBM39).
NEBNext small RNA library prep kit (New England Biolads E7330) NEBNext multiplex oligos; 14 cycles of amplification; after PCR amplification, libraries were purified with Ampure beads XP (1.8x volume of PCR reaction)

value: glioblastoma


title: COLO320, HSR, H3K36me3, rep1

status: Public on May 23 2024

type: SRA

city: Stanford

first: Guiping

last: Wang

address: 256 Campus Dr

country: USA

institute: Stanford University

description: H3K36me3 ChIP-seq

library_source: genomic

data_processing:
The sequence data were trimmed by Trimmomatic22 (v0.36) to remove adapter
Reads were mapped to the hg38 assembly of the human genome using Bowtie2 with the following settings: --local --very-sensitive --phred33 -X 1000.
Reads with MAPQ values less than 10 were filtered using SAMtools (v1.8)
Duplicate reads were removed using picard-tools.
Bigwig (.bw) files were generated for each strand using bamCoverage (py-deeptools/3.3.1_py36) with -binSize 10 --normalizeUsing CPM
Input normalized bigwig (.bw) files were generated using bamCompare default settings.
Assembly: hg38
Supplementary files format and content: Bigwig (.bw) files contain normalized DNA signals  for visualization.
Supplementary files format and content: Bigwig (.bw) files (normalized_log2Ratio) contain CHIP signals normalized to input for visualization.

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: RPMI, 10% FBS, 1% pen/strep

extract_protocol:
Cells were fixed in 1% formaldehyde for 15min with rotation then quenched with 0.125M glycine. After cell membrane lysis and then nuclear lysis, chromatin was sonicated using a Vocariss E220 sonicator (140W, 10% duty, 200 cycles/burst, 600sec/sample).
NEBNext Ultra II DNA library prep kit with NEBNext multiplex oligos; 6 cycles of amplification

tag: chip antibody

value: H3K36me3 abcam ab9052

tag: cell line

tag: cell type

value: colorectal carcinoma


title: bone_O-Ctrl1-CR-14_tech_rep3

city: Nuthetal

first: Tim

middle: Julius

last: Schulz

address: Arthur-Scheunert-Allee 114-116

country: Germany

institute: German Institute of Human Nutrition

library_source: transcriptomic

data_processing:
FastQC (v 0.11.8) and MultiQC (v 1.6) were used to check the quality metrics of the datasets. Reads containing adapter sequences were filtered out using Trim Galore (v 0.5.0). Filtered reads were mapped to the mm10 reference genome using the alignment tools STAR (v 2.6.1). FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values were quantified with StringTie (v 2.1.3b) and count matrix was generated in R (v 4.1.1). Expression values for each gene were averaged from 4 sequencing technical replicates.
Assembly: mm10
Supplementary files format and content: Comma-separated value files

molecule: total RNA

organism: Mus musculus

source_name: bone, old, ctrl

extract_protocol:
Tibia bones were isolated by completely removing adherent muscle and connective tissue, and were immediately frozen in liquid nitrogen and stored at -80°C until further processing. RNA was extracted from whole-tissue, ground to a powder while frozen in liquid nitrogen, using the phenol/chloroform method. Specifically, an aliquot of approximately 50 mg of tissue powder was vortexed for one minute with 200 µl of Trizol (Thermo Fisher Scientific). After centrifugation at 12,000g for 10 minutes at 4°C, supernatant was transferred to a new tube and 40µl of chloroform were added. Samples were centrifuged for 15 minutes at 12,000g and 4°C, followed by RNA precipitation from the collected upper clear phase with 250 μl of isopropanol. RNA was purified by washing in 500 μl of 75% ethanol, dried and solubilized in 30 μl DEPC-treated, i.e. RNAse-free, water. DNase digest of purified RNA was performed using the Invitrogen Turbo DNA-free kit (Thermo Fisher Scientific). An Agilent 2100 BioAnalyzer (Agilent RNA 6000 Nano Kit) was used to check for total RNA quality of the samples.
mRNA was prepared for sequencing using the TruSeq stranded mRNA sample preparation kit (Illumina), with a selected insert size of 120–210 bp, and sequenced on an Illumina HiSeq 4000 instrument.

tag: tissue

value: whole bone

tag: age

value: old

tag: treatment

value: ctrl


title: GBM39, ec, GRO-seq, rep1

description:
GBM39ec_GRO_rep1
GRO-seq


title: ChIP-seq of Pol2 in element B deletion ESC_R2

city: Montpellier

first: Ivana

last: Jerkovic

state: Occitanie

address: 141 rue de la Cardonille

country: France

institute: IGH, CNRS

data_processing:
Data were mapped using bowtie2, the duplicated reads were discarded and bigwigs were produced directly from deduplicated bam files. For detailed protocol see the methods section of the adjoining paper.
Assembly: mm10
Supplementary files format and content: Processed files are given as a bigwig file of the two merged replicates.

growth_protocol: ESC were grown in FBS+LIF media with standard conditions. NPCs were differentiated using retinoic acid between days 4 and 8 when the cells were harvested. For detailed protocol see adjoning paper.

extract_protocol:
Chromatin was fixed with 1% formaldehyde for 10 min at RT. Cells were lysed and IP done using Diagenone iDeal ChIP-seq kit for TFs or histones according to the manufacturer's recommendation.
Libraries were constructed by BGI

value: mESC dB

tag: genotype

value: deletion of element B


title: bone_O-Ctrl1-CR-14_tech_rep4


title: GBM39, HSR, GRO-seq, rep2

description:
GBM39HSR_GRO_rep2
GRO-seq


title: bone_O-CR-7_tech_rep2

source_name: bone, old, calorie restriction

value: calorie restriction


title: ChIP-seq INPUT in element B deletion ESC


title: GBM39, HSR, GRO-seq, rep1

description:
GBM39HSR_GRO_rep1
GRO-seq


title: COLO320, HSR, GRO-seq, rep2

description:
COLO320HSR_GRO_rep2
GRO-seq


title: bone_O-Ctrl1-CR-14_tech_rep2


title: ChIP-seq of Pol2 in element B deletion ESC_R1


title: ChIP-seq of Rad21 in element B deletion ESC_R2


title: COLO320, DM, input, rep1

description: ChIP-seq input


title: COLO320, DM, GRO-seq, rep2

description:
COLO320DM_GRO_rep2
GRO-seq


title: COLO320, HSR, GRO-seq, rep1

description:
COLO320HSR_GRO_rep1
GRO-seq


title: bone_O-Ctrl1-CR-14_tech_rep1


title: ChIP-seq of Rad21 in element B deletion ESC_R1


title: COLO320, DM, GRO-seq, rep1

description:
COLO320DM_GRO_rep1
GRO-seq


title: ChIP-seq of CTCF in element B deletion ESC_R2


title: bone_O-CR-6_tech_rep4


title: ChIP-seq of CTCF in element B deletion ESC_R1


title: bone_O-CR-6_tech_rep2


title: ChIP-seq of H3K36me3 in element B deletion ESC_R2


title: ChIP-seq of H3K36me3 in element B deletion ESC_R1


title: bone_O-CR-6_tech_rep1


title: Illumina_SS_VIC01_48_child_FASTQ

city: Melbourne

first: Jessie

middle: Jie-Youen

last: Chang

address: 792 Elizabeth Street

country: Australia

institute: The Peter Doherty Institute at The University of Melbourne

library_source: transcriptomic single cell

data_processing:
FASTQ reads from individual libraries were analyzed with Cellranger v6.1.1 'count' using the reference package ‘refdata-gex-GRCh38-2020-A’ to visualise the read counts belonging to the host (human). Parameters (r1-length: 28,  r2-length:90, expect cells: 10950 for main samples (MS), 1930 for sub-samples (SS)). The outputs included aligned BAM files as well as the count matrices.
BAM files generated from GRCh38/hg38 were lifted with liftover tool CrossMap v0.5.4 to GRCh37/hg19 to enable incorporation of the donor genotype information which was analyzed using GRCh37. PLINK v1.9 was used to convert the output of the genotyping data to VCF files. The VCF files and the sorted GRCh37 BAM files were used as inputs to Demuxlet v11022021. This enabled the donor assignment to cell barcodes and estimated the number of doublets in the data.
Cellranger reference was created for SARS-CoV-2 reference genome using Cellranger ‘mkref’ using the Ensembl reference ASM985889v3, INSDC Assembly GCA_009858895.3, Jan 2020 and a custom GTF file by setting the whole genome as an exon. Viral counts were determined separately but similarly to host counts using Cellranger ‘count’. Parameters (r1-length: 28,  r2-length:90, expect cells: 17850 for main samples (MS), 3150 for sub-samples (SS)) For the viral counts, raw matrices instead of filtered matrices were utilized for downstream analysis as the effect of filtered matrices (i.e. filtering of artifactual cells) was not applicable to the viral counts.
Assembly: GRCh38
Supplementary files format and content: Tab/space-delimited text file includes Cellranger outputs of filtered_feature_bc_matrix for host and raw_feature_bc_matrix for viral reads for each condition/treatment per age-group (3 donors multiplexed)
Supplementary files format and content: Tab-delimited text file includes Genotyping analysis (best) outputs from Demuxlet v11022021 for each donor in age-group involved in the library

molecule: polyA RNA

growth_protocol: Cells were seeded on to 6.5 mm Transwell inserts pre-coated with PureCol-S collagen type I. Then, the cells were incubated at 37°C and 5% v/v CO2 until confluency in PneumaCultTM-ExPlus media for 4-7 days before being switched to ALI culture conditions by removing the apical media and feeding the basal side with PneumaCultTM ALI medium. The cultures were incubated 3-4 weeks to achieve mucocilliary differentiation.

extract_protocol:
Extraction for scRNA-seq: The ALI-cultured HNECs were prepared according to the 10X Chromium Single Cell Protocols Cell Preparation Guide General Sample Preparation RevC. 7000 cells per donor per condition were multiplexed, resulting in the three donors per age-group being multiplexed into each library. Then, the Chromium Single Cell 3' Reagent Kit v3.1 (dual index protocol) was used for the extraction of the cDNA. Extraction for genotyping: DNeasy Blood and Tissue Kit (Qiagen) with minor modifications.
scRNA-seq: Chromium Single Cell 3' Reagent Kit v3.1 adapted for Full Length Transcriptome-Sequencing (FLT-Seq, Tian et al., 2021).

treatment_protocol: ALI culture infections were carried out with a MOI of 0.014 in 30 µL of inoculum per insert (assuming ~300,000 cell at the surface) with either the ancestral strain (VIC01) or Alpha (VIC17991/UK). After virus adsorption for 2 h at 37°C, the inoculum was washed off with PBS containing calcium and magnesium (PBS++). Samples included a mock-control, ancestral strain-infected 48 hpi, ancestral strain-infected 72 hpi and Alpha variant-infected at 72 hpi per donor.

value: Infected with ancestral strain (VIC01) harvested at 48 hpi


title: bone_O-Ctrl1-CR-13_tech_rep4


title: bone_O-Ctrl1-CR-13_tech_rep3


title: Illumina_SS_VIC01_72_child_FASTQ

value: Infected with ancestral strain (VIC01) harvested at 72 hpi


title: Illumina_MS_VIC01_48_child_FASTQ


title: ChIP-seq of H3K27Ac in element B deletion ESC_R2


title: ChIP-seq of H3K27Ac in element B deletion ESC_R1


title: Illumina_SS_uninfected_child_FASTQ

value: Mock-control


title: ChIP-seq of H3K4me3 in element B deletion ESC_R2


title: bone_O-Ctrl1-CR-13_tech_rep2


title: ChIP-seq of H3K4me3 in element B deletion ESC_R1


title: Illumina_SS_VIC01_48_adult_FASTQ


title: Illumina_SS_uninfected_adult_FASTQ


title: Illumina_SS_UK_72_adult_FASTQ

value: Infected with Alpha variant (VIC17991) harvested at 72 hpi


title: bone_O-CR-5_tech_rep4


title: Illumina_MS_uninfected_child_FASTQ


title: ChIP-seq INPUT in element A deletion NPC

source_name: E14tg2a differentiated into neuronal progenitor cells (NPCs)

value: NPC dA

value: deletion of element A


title: bone_O-CR-6_tech_rep3


title: Illumina_SS_VIC01_72_adult_FASTQ


title: bone_O-CR-5_tech_rep3


title: bone_O-Ctrl1-CR-13_tech_rep1


title: ChIP-seq of Pax6 in element A deletion NPC_R2

value: E14tg2a differentiated into neuronal progenitor cells (NPCs)


title: Illumina_MS_uninfected_adult_FASTQ


title: bone_O-CR-5_tech_rep2


title: Illumina_SS_UK_72_child_FASTQ


title: ChIP-seq of Pax6 in element A deletion NPC_R1


title: PBMC from Pt-23, replicate1, scRNAseq

city: Houston

first: Linghua

address: 1881 East Road,

institute: MD Anderson Cancer Center

data_processing: Sequence data was put through the 10X genomic cell ranger 3.0 pipeline. QC and Fastq files were obtained and checked for data quality, and Fastq files were used to do further analysis.

source_name: PBMC

extract_protocol:
the fresh tissues were stored in the tissue storage solution (MACS Media) and dissociated into single cell suspensions for scRNA-seq. The ascites were spun down for 10 minutes at 1500 rpm, then pelleted cells were collected and stored in Bambanker (Nippon Genetics, no.392014681) for scRNA-seq. PBMCs were separated from peripheral blood according to standardized procedure. Red blood cells were lysed and singlets were counted by Trypan Blue Exclusion before loading on 10X Chromium microfluidic chips.  All sample were processed using the same protocol and by the same research assistant.
The scRNA-seq libraries were constructed using the Chromium Single Cell 5ʹ Library & Gel Bead Kit (PN: 220112, 10 Genomics). The single-cell GEMs were used to generate 10 Barcoded cDNA through reverse-transcription PCR and the cDNA was purified using Dynabeads MyOne SILANE magnetic beads (PN: 2000048, 10 Genomics). The Amplification Master Mix kit (PN: 220125, 10 Genomics) was used for cDNA amplification, and the Beckman Coulter SPRIselect reagent was used for cDNA purification and target enrichment. The Agilent Bioanalyzer High Sensitivity kit was used for determination of concentrations of cDNA libraries as well as the quality control of libraries. 50 ng of each sample library in 20 uL were mixed with 30 uL Fragmentation Mix (PN: 220108, 220107/220130, 10 Genomics) for pooling. The barcoded libraries were sequenced on the NovaSeq 6000 (Illumina) platform using S2 flow cell (100 cycles) in a 26 (read 1) × 8 (index) × 91 (read 2) configuration.

value: PBMC

value: Treatment Naïve


title: Illumina_MS_UK_72_adult_FASTQ


title: bone_O-CR-5_tech_rep1


title: PC from Pt-23, replicate1, scRNAseq

source_name: Peritoneal Ascites

value: Peritoneal Ascites


title: Illumina_MS_VIC01_72_child_FASTQ


title: bone_Y-Ctrl1-CR-11_tech_rep4

source_name: bone, young, ctrl

value: young


title: N from Pt-23, replicate1, scRNAseq

source_name: Normal Adjacent Tissue

value: Normal Adjacent Tissue


title: PRI from Pt-23, replicate1, scRNAseq

source_name: Primary Tumor

value: Primary Tumor


title: Illumina_MS_UK_72_child_FASTQ


title: ChIP-seq of Pol2 in element A deletion NPC_R1


title: PBMC from Pt-22, replicate1, scRNAseq


title: PRI from Pt-22, replicate1, scRNAseq


title: ChIP-seq of Rad21 in element A deletion NPC_R2


title: PC from Pt-22, replicate1, scRNAseq


title: bone_Y-Ctrl1-CR-11_tech_rep3

value: whole bone

value: ctrl


title: bone_Y-Ctrl1-CR-11_tech_rep2


title: Illumina_MS_VIC01_48_adult_FASTQ


title: N from Pt-22, replicate1, scRNAseq


title: PRI from Pt-21, replicate1, scRNAseq


title: ChIP-seq of Rad21 in element A deletion NPC_R1


title: Illumina_MS_VIC01_72_adult_FASTQ


title: PBMC from Pt-21, replicate1, scRNAseq


title: bone_Y-Ctrl1-CR-11_tech_rep1


title: ChIP-seq of CTCF in element A deletion NPC_R2


title: PC from Pt-21, replicate1, scRNAseq


title: N from Pt-21, replicate1, scRNAseq


title: PBMC from Pt-20, replicate1, scRNAseq


title: ChIP-seq of CTCF in element A deletion NPC_R1


title: bone_Y-CR-3_tech_rep4

source_name: bone, young, calorie restriction


title: ChIP-seq of Pol2 in element A deletion NPC_R2


title: LM from Pt-20, replicate1, scRNAseq

source_name: Liver Metastasis

value: Liver Metastasis


title: bone_Y-CR-3_tech_rep3

value: calorie restriction


title: bone_Y-CR-3_tech_rep2


title: ChIP-seq of H3K36me3 in element A deletion NPC_R2


title: bone_Y-CR-3_tech_rep1


title: N from Pt-20, replicate1, scRNAseq


title: PBMC from Pt-19, replicate1, scRNAseq


title: ChIP-seq of H3K36me3 in element A deletion NPC_R1


title: bone_Y-Ctrl1-CR-10_tech_rep4


title: PRI from Pt-18, replicate1, scRNAseq


title: bone_Y-Ctrl1-CR-10_tech_rep3


title: PBMC from Pt-18, replicate1, scRNAseq


title: LM from Pt-18, replicate1, scRNAseq


title: ChIP-seq of H3K27Ac in element A deletion NPC_R1


title: ChIP-seq of H3K4me3 in element A deletion NPC_R2


title: PC from Pt-19, replicate1, scRNAseq


title: N from Pt-18, replicate1, scRNAseq


title: ChIP-seq of H3K4me3 in element A deletion NPC_R1


title: PRI from Pt-17, replicate1, scRNAseq


title: bone_Y-Ctrl1-CR-10_tech_rep1


title: PRI from Pt-20, replicate1, scRNAseq


title: N from Pt-17, replicate1, scRNAseq


title: PRI from Pt-16, replicate1, scRNAseq


title: bone_Y-Ctrl1-CR-10_tech_rep2


title: PRI from Pt-19, replicate1, scRNAseq


title: ChIP-seq of Pol2 in element A deletion ESC_R2

value: mESC dA


title: PRI from Pt-15, replicate1, scRNAseq


title: N from Pt-16, replicate1, scRNAseq


title: bone_Y-CR-2_tech_rep3


title: N from Pt-19, replicate1, scRNAseq


title: ChIP-seq of H3K27Ac in element A deletion NPC_R2


title: PBMC from Pt-14, replicate1, scRNAseq


title: ChIP-seq of Pol2 in element A deletion ESC_R1


title: N from Pt-15, replicate1, scRNAseq


title: PRI from Pt-14, replicate1, scRNAseq


title: LM from Pt-14, replicate1, scRNAseq


title: ChIP-seq of Rad21 in element A deletion ESC_R2


title: bone_Y-CR-2_tech_rep1


title: bone_Y-CR-2_tech_rep2


title: bone_Y-Ctrl1-CR-9__tech_rep4


title: PBMC from Pt-13, replicate1, scRNAseq


title: ChIP-seq of Rad21 in element A deletion ESC_R1


title: N from Pt-14, replicate1, scRNAseq


title: ChIP-seq of CTCF in element A deletion ESC_R2


title: LM from Pt-17, replicate1, scRNAseq


title: PRI from Pt-13, replicate1, scRNAseq


title: ChIP-seq INPUT in element A deletion ESC


title: bone_Y-Ctrl1-CR-9__tech_rep3


title: bone_Y-CR-2_tech_rep4


title: PC from Pt-13, replicate1, scRNAseq


title: N from Pt-13, replicate1, scRNAseq


title: ChIP-seq of CTCF in element A deletion ESC_R1


title: bone_Y-Ctrl1-CR-9__tech_rep2


title: PRI from Pt-12, replicate1, scRNAseq


title: LM from Pt-12, replicate1, scRNAseq


title: ChIP-seq of H3K36me3 in element A deletion ESC_R2


title: PBMCfrom Pt-11, replicate1, scRNAseq


title: ChIP-seq of H3K36me3 in element A deletion ESC_R1


title: PB from Pt-11, replicate1, scRNAseq

source_name: Peripheral Blood

value: Peripheral Blood


title: ChIP-seq of H3K27Ac in element A deletion ESC_R2


title: bone_Y_CR1_tech_rep4


title: PC from Pt-11, replicate1, scRNAseq


title: PBMC from Pt-10, replicate1, scRNAseq


title: bone_Y_CR1_tech_rep3


title: ChIP-seq of H3K27Ac in element A deletion ESC_R1


title: bone_Y_CR1_tech_rep2


title: ChIP-seq of H3K4me3 in element A deletion ESC_R2


title: PRI from Pt-10, replicate1, scRNAseq


title: bone_Y_CR1_tech_rep1


title: LM from Pt-10, replicate1, scRNAseq


title: N from Pt-10, replicate1, scRNAseq


title: ChIP-seq of H3K4me3 in element A deletion ESC_R1


title: SPL_WT83

city: New York

first: Teresina

last: Laragione

state: NY

address: 1468 Madison Ave

department: Medicine

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. Inthis step, clean data (clean reads) were obtained by removing reads containing adapter, readscontaining ploy-N and low quality reads from raw data. At the same time, Q20, Q30andGCcontent the clean data were calculated. All the downstream analyses were based on thecleandata with high quality
Remove reads with adapter contamination.
Remove reads when uncertain nucleotides constitute more than 10 per cent of either read (N > 10%).
Remove reads when low-quality nucleotides (Base Quality less than 5) constitute more than 50 per cent of the read.
Perform alignments withHISAT2to the reference
Assembly: Hg38
Supplementary files format and content: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. Andthen FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depthandgene length for the reads count at the same time, and is currently the most commonlyusedmethod for estimating gene expression levels.
Supplementary files format and content: Tab-delimited text file includes fpkm for each sample

source_name: Spleen

growth_protocol: DUSP6 KO (Dusp6tm1Jmol) and WT mice were purchased from the Jackson Laboratories  and housed under specific pathogen-free conditions.

extract_protocol:
Total RNAextracted from five different spleens from WT and five from DUSP6 KO mice by Qiagen RNAeasy kit, and quantified by Nanodrop. 400 ng per tissue per mouse was sent to Novogene (Beijing, China) for sequencing and analyses
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using randomhexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional libraryor dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, sizeselection, amplification, and purificationFor the directional library, it was ready after end repair, A-tailing, adapter ligation, sizeselection, USER enzyme digestion, amplification, and purification.The library was checked with Qubit and real-time PCR for quantification and bioanalyzer forsize distribution detection. Quantified libraries will be pooled and sequenced on Illuminaplatforms, according to effective library concentration and data amount. The clustering of the index-coded samples was performed according to the manufacturer’sinstructions. After cluster generation, the library preparations were sequenced on an Illuminaplatform and paired-end reads were generated

treatment_protocol: Arthritogenic serum was collected from the 60-day-old arthritic offspring of KRN x NOD F1 cross. Serum from different batches was pooled and administered to Male and female DUSP6-KO and WT mice at 100 µL IP on days 0 and 2. Mice spleen were collected at day 9 (arthritis peak).

value: Spleen

value: WT

value: KRN serum induced arthritis (KSIA)


title: scATAC_mEBs_d21_crispri_rep2_lane_b

city: Montreal

first: Jean-Benoit

last: Lalanne

state: QC

address: 5155 Chem. de la Rampe

department: Biochemistry and Molecular Medicine

country: Canada

institute: University of Montreal

description: 10x Genomics scATAC-seq

data_processing:
Fastq files were generated by running cellranger makefastq. The resulting fastq files were then processed to fragment files using 10x Genomics cellranger count (cellranger-atac-cs version 1.2.0, reference = refdata-cellranger-atac-mm10-1.2.0), which were processed through the ArchR pipeline. Arrow files were created with function createArrowFiles (minTSS=4, minFrags=1000). Two different double scores were computed with function addDoubletScores (LSI based: k=10, knnMethod=”LSI”, LSIMethod=1); UMAP based: k=10, LSImet=1, UMAPparam: n_neighbors=40, min_dist=0.4, metric=”euclidiean”). In addition, we used AMULET (from its v1.0-beta version, running function ATACDoubletDetector.py and adding as problematic region a union of the ENCODE excluded list, segmental duplications, simple repeats, repeat masker, and microsatellites from mm10 obtained from UCSC). Nuclei were then filtered for: TSS enrichment >8 and >1995 fragment counts. Following dimensional reduction (addIterativeLSI: useMatrix = "TileMatrix", name = "IterativeLSI", iterations = 2, varFeatures = 100000, dimsToUse = 1:30), and clustering (AddClusters: reducedDims = "IterativeLSI", method = "Seurat", name = "Clusters", resolution = 0.5), doublets were stringently removed by inspecting distribution of fragment counts, doublet scores (ArchR derived), and AMULET doublet scores per clusters. All nuclei from clusters with anomalously high doublet scores across metrics were removed. In addition, individual nuclei with either >17782 fragment counts, LSI doublet score > 0, UMAP doublet score > 0, or AMULET score > 0.3 (thresholds assessed from the distribution of anomalous doublet clusters) were removed. In the end, 31% of nuclei were removed with these filters, leaving 46408 nuclei passing quality filters (20329 nuclei from replicate 1, 26079 nuclei from replicate 2).  The resulting filtered nuclei were dimensionally reduced and clustered (same parameters as above), leading to 9 clusters with >200 nuclei. Clusters with highly correlated accessibility over all peaks (averaged over all cells per cluster, R2 on log-transformed accessibility >0.55) and proximal in the low-dimensional projection were merged. The intermediate endoderm cluster (connecting the visceral and parietal clusters) was kept separate to avoid diluting the signal from the two well-delineated clusters.
Assembly: mm10
Supplementary files format and content: scATAC pseudobulk pileup bw files for these clusters were generated using ArchR’s function getGroupBW (normMethod=“ReadsInTSS”, tileSize=50, maxCells=1E5, ceiling=10).  scATAC_mEB_d21_pseudobulk_accessibility_per_cluster: column 1: unique peak id; column 2: chromosome; column 3: peak start; column 4: peak end; column 5: ArchR peak score; column 6 to 12: normalized mean peak accessibility per cluster (count per cell per peak is normalized by number of reads in TSS, and averaged over all cells in respective cluster).

source_name: WD44 (mouse embryonic stem cells)

growth_protocol: Exponentially growing mESCs are lifted from the plate (aspirate medium, wash with PBS, add 2.5 mL [for 10 cm plate] 0.05% trypsin , incubate 2 minutes at 37C, deactivate trypsin and triturate to a single-cell suspension with 10 mL pre-warmed SL medium). Cells are then counted and spun down (5 min at 300 g). Supernatant is aspirated and cells are resuspended to 2 M/mL in CA medium (medium for EB induction: DMEM, 10% FBS, 1x MEM non-essential amino-acids, 1x Glutamax , 10-5 beta-mercaptoethanol). Cells are counted again, and density adjusted to 1 M/mL with CA medium. 3 mL (3 M cells) are added to 12 mL of CA medium in 10 cm plates (non gelatinized, non adherent). One the next day, plates are gently agitated to promote cell aggregation.   Following induction, embryoid bodies (mEBs) are passaged every two days (no daily medium change). mEBs are collected using a serological pipette and transferred to a 50 mL conical tube (typically three plates are pooled). Leftover mEBs on plates are recovered by a CA medium wash and pooled with in the conical tube. mEBs are left to settle (initially up to 15-20 min, faster as the mEBs grow in size). Once mEBs have settled, medium is aspirated from the top, carefully avoiding disturbing the loose pellet. Fresh, pre-warmed, CA medium is then added to 15 mL/plate and mEBs redistributed to plates.

extract_protocol:
Single-nuclei preparation for scATAC-seq were prepared from day 21 mEB as follows: At day 21 of mEB cultures, mEBs (2X 10cm suspension plates) are collected into a 50 mL conical tube and washed 2X with 1X PBS (w/o Ca, Mg). After consecutive PBS washes, mEBs are treated with 1.5mL of 0.25% trypsin and incubated in 37C bath with gentle agitation (steady concentric swirls of 50mL concial) for 3 minutes. For further dissociation, mEBs are then gently titurated 10X with a p1000 pipette. Again, incubate at 37C for 3 minutes with gentle agitation. After second incubation, mEBs are gently titurated 10X with a p1000 pipette. Inactivate trypsin digestion with CA medium and filter single cell suspension through a 100um filter into new 50mL conical. Count single cell suspension and aim for >>100K total cells. Spin 50mL conical tube at 300g for 5 minutes. After removing supernatant, wash 1X with 1mL of 1X PBS + 0.04% BSA and gently pipette mix 5X. Transfer to a 1.5 mL tube and spin at 300g for 5 min at 4C. Wash again with 1mL of 1X PBS + 0.04% BSA. Again,  spin at 300g for 5 min at 4C. Proceed with 10x "Nuclei isolation for Single Cell ATAC Sequencing" protocol.
scATAC-seq libraries were prepared following 10x Genomics protocol in "Chromium Next GEM Single Cell ATAC Reagent Kits v1.1".  Read structure: read 1 50 cycles, index 1 8 cycles, read 2 50 cycles, index 2 16 cycles

value: WD44 (mouse embryonic stem cells)

value: Mouse embryoid bodies

value: monoclonal CRISPRi (cAS9-KRAB) cell line

value: Day 21


title: SPL_WT77


title: ChIP-seq INPUT in polyA insertion at Zfp608 NPC

value: E14tg2a differentiated into neuronal progenitor cells (NPCs)

value: NPC polyA

value: polyA insertion at Zfp608 TSS


title: N from Pt-12, replicate1, scRNAseq

value: Normal Adjacent Tissue

value: Treatment Naïve


title: scATAC_mEBs_d21_crispri_rep1_lane_b

description: 10x Genomics scATAC-seq


title: scATAC_mEBs_d21_crispri_rep2_lane_a

description: 10x Genomics scATAC-seq


title: ChIP-seq of Pax6 in polyA insertion at Zfp608 NPC_R2


title: SPL_WT67


title: PRI from Pt-9, replicate1, scRNAseq

value: Primary Tumor


title: SPL_WT73


title: bone_Y-Ctrl1-CR-9__tech_rep1

value: whole bone

value: young

value: ctrl


title: OV from Pt-11, replicate1, scRNAseq

source_name: Ovarian Metastasis

value: Ovarian Metastasis


title: LM from Pt-9, replicate1, scRNAseq

value: Liver Metastasis


title: PB from Pt-10, replicate1, scRNAseq

value: Peripheral Blood


title: SPL_WT65

value: Spleen

value: WT

value: KRN serum induced arthritis (KSIA)


title: ChIP-seq of Pax6 in polyA insertion at Zfp608 NPC_R1


title: N from Pt-9, replicate1, scRNAseq


title: ChIP-seq of Pol2 in polyA insertion at Zfp608 NPC_R2


title: ChIP-seq of Pol2 in polyA insertion at Zfp608 NPC_R1


title: DEX+Y26

city: Shanghai

first: Jinhai

last: Huang

address: 83 Fenyang Road, Xuhui District

country: China

institute: EYE & ENE Hospital of Fudan University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latestiwhat-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix filesTab-separated values files and matrix files

source_name: 1mm before and after the ora serrata

extract_protocol: 10 weeks after mold and virus injection, eyes were surgically removed from the mice and trimmed, then surgical scissors were used to take samples 1mm before and after the ora serrata immediately and kept in a special preservation solution. All operations were performed on ice. The samples were delivered to CapitalBio Technology (Beijing, China) and sequenced for analysis.

treatment_protocol: 10 μl of DEX-Ac (Aladdin, China) suspension was injected under the fornix conjunctiva of both eyes with a 29G insulin needle every 7 days for the duration of each experiment to establish the ocular hypertension mice model. ShH10 Y26 virus were  injected intravitreally 3 days after the induction of the ocular hypertension model. Ten weeks post-virus injection, the eyes were surgically removed from the mice, trimmed, and samples were taken 1mm before and after the ora serrata using surgical scissors. These samples were immediately preserved in a specialized solution and all operations were conducted on ice. The samples were subsequently sent to CapitalBio Technology (Beijing, China) for sequencing and analysis.

value: 1mm before and after the ora serrata

value: Goblet cells

tag: strain

value: 18 weeks old

value: ShH10 Y26 virus injection


title: SPL_HOM03

value: DUSP6 Knockdown


title: PRI from Pt-5, replicate1, scRNAseq


title: SPL_HOM01


title: ChIP-seq of Rad21 in polyA insertion at Zfp608 NPC_R2

value: E14tg2a differentiated into neuronal progenitor cells (NPCs)

value: NPC polyA

value: polyA insertion at Zfp608 TSS


title: OV from Pt-5, replicate1, scRNAseq

value: Treatment Naïve


title: ChIP-seq of Rad21 in polyA insertion at Zfp608 NPC_R1


title: DEX+NS

description: 10x Genomics

treatment_protocol: 10 μl of DEX-Ac (Aladdin, China) suspension was injected under the fornix conjunctiva of both eyes with a 29G insulin needle every 7 days for the duration of each experiment to establish the ocular hypertension mice model. Normal saline (NS) was  injected intravitreally 3 days after the induction of the ocular hypertension model. Ten weeks post-virus injection, the eyes were surgically removed from the mice, trimmed, and samples were taken 1mm before and after the ora serrata using surgical scissors. These samples were immediately preserved in a specialized solution and all operations were conducted on ice. The samples were subsequently sent to CapitalBio Technology (Beijing, China) for sequencing and analysis.

value: Normal saline (NS) injection


title: SPL_HOM73


title: SPL_HOM21


title: PC from Pt-5, replicate1, scRNAseq

value: Peritoneal Ascites


title: N from Pt-5, replicate1, scRNAseq

value: Normal Adjacent Tissue


title: scATAC_mEBs_d21_crispri_rep1_lane_a

description: 10x Genomics scATAC-seq

value: WD44 (mouse embryonic stem cells)

value: Mouse embryoid bodies

value: monoclonal CRISPRi (cAS9-KRAB) cell line

value: Day 21


title: SPL_HOM26

value: Spleen

value: KRN serum induced arthritis (KSIA)


title: ChIP-seq of CTCF in polyA insertion at Zfp608 NPC_R2


title: ChIP-seq of CTCF in polyA insertion at Zfp608 NPC_R1


title: Zygote Sl Expt. 3 - Sample 03

city: København

first: Jason

middle: A

last: Halliwell

address: Blegdamsvej 3B

country: Denmark

institute: The University of Copenhagen

data_processing:
Raw sequencing reads were trimmed, aligned and processed according to Miura et al., 2020 (PMID: 33230331).
Data processing of trimmed abd aligned reads were processed to obtain log2 fold replication timing values according to the methodology described by Miura et al. in their publication from 2020 (PMID: 33230331).
Assembly: mm10
Supplementary files format and content: BedGraph

source_name: Zygote

growth_protocol: To obtain zygotes and 2-cell stage embryos, four to eight-week-old donors were injected with 100µl of 50 I.U. ml-1 (international units) ml−1 solution) solution pregnant mare serum gonadotropin (PMSG) at 17.00 followed by injection of 100µl of 50 I.U. ml-1 human chorionic gonadotropin (hCG) at 17.00 48 hours after PMSG. Mouse ES cells were cultured on 6-well plates, which had been coated with 0.01% poly-L-ornithine for 1 hours followed by 10 ng/ml-1 laminin for a further hour. The cells were maintained in 2i + LIF and passaged every 3-4 days using TrypLE dissociation solution.

extract_protocol:
DNA extraction for single-cell RepliSeq was conducted following established protocols as described in a previous publication (PMID: 33230331).
Library construction was carried out using the protocols established by Miura et al., 2020 (PMID: 33230331), incorporating IDT for Illumina unique dual indexes and the KAPA Hyper Prep Kit from Roche.
single cell RepliSeq

treatment_protocol:
In Vitro Ferilized embryos were maintained in KSOM.
To obtain synchronized 2-cell stage embryos, zygotes were collected 16 hours post fertilization. Subsequently, they were incubated in a 40 nM Nocodazole solution for 4 hours, following which they were washed to facilitate release.
Mouse ES cells were sorted using FACS cytometry and prepared for RepliSeq based on a previously published protocol (PMID: 31406346).

value: Zygote


title: PRI from Pt-4, replicate1, scRNAseq

value: Primary Tumor


title: naïve splenic NK - HSF1-S303/7A; HSF1 IP

first: Kathryn

middle: Grace

last: Hockemeyer

state: New York

address: 550 1st Avenue

department: Pathology

institute: NYU Langone Health

data_processing:
Reads were trimmed for adapter sequences and low-quality score bases using Trimmomatic; reads that were properly paired and had a unique alignment (mapping quality > 30) were retained
Trimmed reads were aligned to the Mus musculus genome (mm10/GRCm38) using the Bowtie2 aligner (v2.3.4.1)
Duplicate reads were removed using sambamba markdup.
Peaks were determined algorithmically using Model-based Analysis of ChIP-Seq 2 algorithm (v1.4.2) with q < 0.05
Peak annotation was performed using ChIPSeeker
Assembly: mm10
Supplementary files format and content: Preprocessed bed files for HSF1 ChIPmentation of HSF1-WT and HSF1-S303/7A primary NK cells with peaks determined algorithmicaly using MACS 2 with q < 0.05

source_name: splenic NK cells

extract_protocol:
Single-cell suspension of splenocytes was enriched for NK using the NK Cell Isolation Kit, mouse (Miltenyi). NK cells from 5 mice served as each biological replicate. The total cell recovered from each were used (1 million cells from WT mice and 600,000 cells from HSF1-S303/7A mice).
Naïve splenic NK cells isolated using the were counted, washed once in PBS and crosslinked in 1% formaldehyde diluted in PBS for 10’ at room temperature. After quenching with glycine, cells were washed once in PBS and snap frozen in aliquots of 106 cells. Each aliquot was incubated for 20’ on ice using 110ul of lysis buffer (50 mM Hepes pH 7.5, 140mM NaCl, 1 mM EDTA, 1% SDS, 0.1% Na-Deoxycholate, 1% Triton X-100) and sonicated using a Covaris R230 instrument using 96 microTUBE Plates (PN 520078). After a clearing step (10’ 16000g 4C) samples were diluted 1:10 with IP dilution buffer (same as lysis without SDS) and precleared for 1 hr with 25ul Protein A Dynabeads (Thermo #10002D) washed three times in blocking buffer (1x PBS + 0.5% BSA). Primary antibodies were added and incubated overnight at 4C on rotation (anti-HSF1 from CST #4356). The next day, 25ul Dynabeads Protein A preblocked overnight were added to each sample and incubated at 4C for 2hrs. Beads were washed twice with each of these buffers, incubating 3’ at 4C on rotation: Low salt wash buffer (0.1% SDS, 1 % Triton X 100, 2 mM EDTA pH 8, 20 mM Tris-Cl pH 8, 150mM NaCl); High salt wash buffer (0.1% SDS, 1 % Triton X 100, 2 mM EDTA pH 8, 20 mM Tris-Cl pH 8, 500mM NaCl); LiCl wash buffer (1%NP40, 0.5% NaDOC, 250mM LiCl, 1mM EDTA pH8, 10mM Tris-Cl pH 8); TE buffer (10mM Tris-Cl pH 8, 1mM EDTA pH8). After last wash and removal of traces of TE buffer, beads were resuspended in 30ul tagmentation mix (14ul H2O, 15ul tagmentation buffer 2x and 1ul Tn5 from Illumina #20034197) and incubated for 5’ at 37C with 800rpm shaking. To stop the reaction, 500ul Low Salt Wash buffer was added and incubated for 5’ on ice. Beads were washed once more with Low Salt WB and 2 other times with TE buffer. After removing any leftover, beads were resuspended in 100ul ChIP elution buffer (50mM Tris HCl pH 8, 10mM EDTA pH 8, 1%SDS) and 2ul of proteinase K (20mg/ml). After overnight incubation at 65C 1400rpm, DNA was purified by adding 180 SPRIselect beads (Beckman Coulter #B23318) and after 2 washes with 80% Ethanol, it was eluted with 22ul of low salt TE buffer (10mM Tris HCl pH8, 0.1mM EDTA pH8). 2ul of DNA were used for a pre-amplification qPCR to estimate the correct number of PCR cycles for library amplification, which was performed using NEBNext® High-Fidelity 2X PCR Master Mix (NEB # M0541S) and Nextera custom primers (IDT) from Buenrostro et al., Nature Methods, 201361. Final libraries were purified (1.8x) and size selected (0.65x) using SPRIselect beads and their size distributions and concentration analyzed using D1000 Agilent High Sensitivity ScreenTapes (#5067-5584). Libraries were sequenced on Novaseq X with 300 cycle lane using 150-bp paired-end reads.

treatment_protocol: Spleens were isolated from mice wild-type (WT) for HSF1 or those bearing serine to alanine mutations in amino acids 303 and 307 (S303/7A or MUT) under steady state conditions

value: splenic NK cells

value: HSF1 immunoprecipitation followed by ChIPmentation


title: ChIP-seq of H3K36me3 in polyA insertion at Zfp608 NPC_R2

value: E14tg2a differentiated into neuronal progenitor cells (NPCs)


title: PBMC from Pt-5, replicate1, scRNAseq

value: PBMC


title: Zygote Sl Expt. 3 - Sample 01


title: ChIP-seq of H3K36me3 in polyA insertion at Zfp608 NPC_R1

value: NPC polyA

value: polyA insertion at Zfp608 TSS


title: Zygote Sl Expt. 3 - Sample 02


title: Zygote Sm Expt. 3 - Sample 03


title: ChIP-seq of H3K27Ac in polyA insertion at Zfp608 NPC_R2


title: DEX+Y25

description: 10x Genomics

treatment_protocol: 10 μl of DEX-Ac (Aladdin, China) suspension was injected under the fornix conjunctiva of both eyes with a 29G insulin needle every 7 days for the duration of each experiment to establish the ocular hypertension mice model. ShH10 Y25 virus were injected intravitreally 3 days after the induction of the ocular hypertension model. Ten weeks post-virus injection, the eyes were surgically removed from the mice, trimmed, and samples were taken 1mm before and after the ora serrata using surgical scissors. These samples were immediately preserved in a specialized solution and all operations were conducted on ice. The samples were subsequently sent to CapitalBio Technology (Beijing, China) for sequencing and analysis.

value: 1mm before and after the ora serrata

value: Goblet cells

value: 18 weeks old

value: ShH10 Y25 virus injection


title: naïve splenic NK - WT; HSF1 IP

value: wild-type


title: Sham

city: Nanjing

first: Ning

last: Li

address: Nanjing

institute: Southeast University

data_processing:
The cleaned raw FASTQ files underwent alignment to the mm10 reference genome and quantification using CellRanger (Version 6.0).
Assembly: mm10
Supplementary files format and content: Tab-separated value files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: kidney

extract_protocol:
Each kidney sample from three mice was minced and digested using the MultiTissue dissociation kit (Miltenyi, 130-110-203), followed by homogenization throsyringe-based mechanical disruption. The kidney tissue was enzymatically digested using a mixture of collagenase I, collagenase IV, and hyaluronidase in 1640 me (Gibco, USA) at 37°C for 40 minutes while suppressing the response with 10% fetal bovine serum (FBS). The resulting dissociated solution was passed through 70-μm cell strainer and then was centrifuged at 400g for 5min at 4℃ to collect the cell pellet. To remove any remaining erythrocytes, the red blood cell (RBC) lysis solution (Miltenyi,130-094-183) was applied on ice. Finally, the single-cell suspension was obtained with over 90% viability as detected by Countstar.
This process was performed by CapitalBio Technology in Beijing. The harvested cell suspension was processed with the Chromium single Cell G Chip Kit (10x Genomics). The reverse transcription was performed with the S1000TM Touch Thermal Cycler (Bio Rad) following a procedure of 53°C for 45 minutes, 85°C for 5 minutes and a subsequent hold at 4°. The official library kit (Single Cell 3' Library and Gel Bead Kit V3.1) was applied to construct the libraries intended for single-cell RNA-seq analysis.

value: kidney

value: Goblet cell

tag: condition

value: Sham


title: PC from Pt-3, replicate1, scRNAseq

value: Peritoneal Ascites

value: Treatment Naïve


title: Zygote Sm Expt. 3 - Sample 02

value: Zygote


title: ChIP-seq of H3K27Ac in polyA insertion at Zfp608 NPC_R1


title: ChIP-seq of H3K4me3 in polyA insertion at Zfp608 NPC_R2


title: AKI day 28

description: UIR murine model of AKI

value: AKI

tag: time point

value: Day 28


title: naïve splenic NK - WT; input

description: Input

value: splenic NK cells

value: input followed by ChIPmentation


title: Zygote Sl Expt. 3 - Sample 04


title: Zygote Sm Expt. 3 - Sample 01


title: PBMC from Pt-2, replicate1, scRNAseq

value: PBMC


title: AKI day 14

description: UIR murine model of AKI

value: Day 14


title: PRI from Pt-2, replicate1, scRNAseq

value: Primary Tumor


title: Zygote Se Expt. 3 - Sample 02


title: Zygote Se Expt. 3 - Sample 01


title: ChIP-seq of H3K4me3 in polyA insertion at Zfp608 NPC_R1

value: E14tg2a differentiated into neuronal progenitor cells (NPCs)

value: NPC polyA

value: polyA insertion at Zfp608 TSS


title: PC from Pt-2, replicate1, scRNAseq


title: PC from Pt-4, replicate1, scRNAseq


title: Zygote G1 Expt. 3 - Sample 04


title: AKI day 1

description: UIR murine model of AKI

value: Day 1


title: ChIP-seq INPUT in polyA insertion at Zfp608 ESC

value: mESC polyA


title: AKI day 3

description: UIR murine model of AKI

value: kidney

value: Goblet cell

value: Day 3


title: PRI from Pt-1, replicate1, scRNAseq

value: Treatment Naïve


title: ChIP-seq of Pol2 in polyA insertion at Zfp608 ESC_R2


title: N from Pt-1, replicate1, scRNAseq

value: Normal Adjacent Tissue


title: PRI from Pt-3, replicate1, scRNAseq


title: RNA-seq of element A and B deletion in mouse NPC_R2

data_processing:
Data were mapped using STARaligner, the reads were counted using subread package. Bigwigs were produced directly from deduplicated bam files. For detailed protocol see the methods section of the adjoining paper.
Assembly: mm10
Supplementary files format and content: Processed files are given as a bigwig file of the two merged replicates.

extract_protocol:
RNA was extracted usint Rnaeasy mini Qiagen kit with RLT buffer supplemented with 2-mercaptoethanol and on-column DNaseI digestion,
Libraries were done by rRNA depletion and constructed by Novogene.

value: NPC dAB

value: double deletion of elements A and B


title: Zygote G1 Expt. 3 - Sample 03

value: Zygote


title: RNA-seq of element A and B deletion in mouse NPC_R1


title: Zygote G1 Expt. 3 - Sample 01


title: ChIP-seq of Rad21 in polyA insertion at Zfp608 ESC_R2


title: ChIP-seq of Pol2 in polyA insertion at Zfp608 ESC_R1


title: ChIP-seq of Rad21 in polyA insertion at Zfp608 ESC_R1


title: Huh7.Ctrl_rep2

city: Beijing

first: Jie

state: Beijing

address: Tsinghua University

department: Basic Medical Sciences, School of Medicine

institute: Tsinghua University

description:
Huh7.Ctrl_rep2
Counts_Huh7.txt

data_processing:
Illumina Casava software was used for basecalling.
Reads were trimmed with the Trim Galore (v0.6.7) software with the default parameters. Then adaptor-trimmed paired-end RNA-seq reads were mapped to GRCh38 human genome using hisat2 (v2.2.1) with default parameters. The read counts were calculated using featurecount (v2.0.3) with extra parameters -O -t exon apart from the default parameters.
Assembly: GRCh38
Supplementary files format and content: Text files of gene names and read counts for each sample.

source_name: cultured cells

growth_protocol: H1 cells were maintained on Growth Factor Reduced Matrigel-coated well plates in TeSR-E8 medium. Huh7 cells were routinely maintained in DMEM medium containing 10% (v/v) FBS, 1% (v/v) GlutaMAX Supplement and 100U/mL Pen Strep. Cryopreserved pHH were cultured in type I collagen coated 24-well plate in OptiPlate hepatocyte medium.

extract_protocol:
Total RNA was extracted using TRIzol acrroding to the instruction mannual.
RNA-seq library was prepared following the Smart-seq2 protocol (Picelli, 2014)

treatment_protocol: For monolayer based macrophage differentiation, pluripotent stem cells were first cultured in E8 medium, after replating, E8 medium was changed to RPMI1640 medium with AATS supplement without insulin, supplemented with BMP4 in the first day and with BMP4 and CHIR99021 in the following 2 days. After 3 days of induction, cells were replated and cultured in RPMI1640 medium with RPMI1640 mainly supplemented with B27 supplement, VEGF, and bFGF. After 2-day induction, SB431542 was added. After another 3 days of induction, floating CD34+CD43+ cells were collected as HSPCs. The HSPCs were further induced in RPMI1640 mainly supplemented with B27 supplement, M-CSF, and IL-3 for 6 days, and all cells were collected and cultured in RPMI1640 with FBS and M-CSF added for more than 2 days. And the mature iMacs were obtained as the adherent cells in the culture. Then  iMacs were subjected to co-cultures with Huh7 cells or pHHs according to different assay design.

value: cultured cells

value: hepatocyte-derived cancer cell line

tag: passage number


title: RNA-seq of element B deletion in mouse NPC_R1

source_name: E14tg2a differentiated into neuronal progenitor cells (NPCs)

value: NPC dB

value: deletion of element B


title: Huh7.Ctrl_rep1

description:
Huh7.Ctrl_rep1
Counts_Huh7.txt


title: ChIP-seq of CTCF in polyA insertion at Zfp608 ESC_R2


title: iMAC.Ctrl_for_Huh7_rep2

description:
iMAC.Ctrl_for_Huh7_rep2
Counts_Huh7.txt

value: human embryonic stem cell line H1-derived macropahge-like cells


title: RNA-seq of element A deletion in mouse NPC_R2

value: E14tg2a differentiated into neuronal progenitor cells (NPCs)

value: NPC dA

value: deletion of element A


title: ChIP-seq of CTCF in polyA insertion at Zfp608 ESC_R1

value: mESC polyA

value: polyA insertion at Zfp608 TSS


title: Zygote Sl Expt. 2 - Sample 02


title: Zygote Sl Expt. 2 - Sample 01


title: RNA-seq of element B deletion in mouse NPC_R2


title: iMAC.Ctrl_for_Huh7_rep1

description:
iMAC.Ctrl_for_Huh7_rep1
Counts_Huh7.txt


title: ChIP-seq of H3K36me3 in polyA insertion at Zfp608 ESC_R2


title: RNA-seq of element A deletion in mouse NPC_R1


title: RNA-seq of polyA insertion at Zfp608 in mouse NPC_R2

value: NPC polyA


title: co.iMac_RFP-_rep2

description:
co.iMac_RFP-_rep2
Counts_Huh7.txt


title: co.Huh7_RFP+_rep2

description:
co.Huh7_RFP+_rep2
Counts_Huh7.txt


title: Zygote Se Expt. 2 - Sample 04


title: RNA-seq of polyA insertion at Zfp608 in mouse NPC_R1


title: ChIP-seq of H3K27Ac in polyA insertion at Zfp608 ESC_R2


title: ChIP-seq of H3K36me3 in polyA insertion at Zfp608 ESC_R1


title: Zygote Se Expt. 2 - Sample 01


title: co.Huh7_RFP+_rep1

description:
co.Huh7_RFP+_rep1
Counts_Huh7.txt


title: RNA-seq of Zfp608 promoter deletion in  mouse NPC_R2

value: NPC dprom

value: deletion Zfp608 promoter


title: Zygote Sm Expt. 1 - Sample 02


title: ChIP-seq of H3K27Ac in polyA insertion at Zfp608 ESC_R1


title: co.iMac_RFP-_rep1

description:
co.iMac_RFP-_rep1
Counts_Huh7.txt


title: Zygote Sm Expt. 2 - Sample 02


title: Zygote Sl Expt. 2 - Sample 05


title: Zygote Sm Expt. 1 - Sample 01


title: ChIP-seq of H3K4me3 in polyA insertion at Zfp608 ESC_R2


title: RNA-seq of Zfp608 promoter deletion in  mouse NPC_R1


title: co.iMac+HCV_rep2

description:
co.iMac+HCV_rep2
Counts_Huh7.txt


title: RNA-seq of wt mouse NPC_R2

value: NPC wt

value: Wild type


title: co.Huh7+HCV_but_uninfected_GFP-_rep2

description:
co.Huh7+HCV_but_uninfected_GFP-_rep2
Counts_Huh7.txt


title: RNA-seq of wt mouse NPC_R1


title: ChIP-seq of H3K4me3 in polyA insertion at Zfp608 ESC_R1


title: ChIP-seq INPUT in Zfp608 promoter deletion NPC


title: co.Huh7+HCV_infected_GFP+_rep2

description:
co.Huh7+HCV_infected_GFP+_rep2
Counts_Huh7.txt


title: Zygote G1 Expt. 1 - Sample 03


title: ChIP-seq of Pax6 in Zfp608 promoter deletion NPC_R2


title: co.iMac+HCV_rep1

description:
co.iMac+HCV_rep1
Counts_Huh7.txt


title: Zygote G1 Expt. 1 - Sample 02


title: RNA-seq of Pax6 upregulation in mouse ESC_R2

value: mESC upPAX6

value: Pax6 upregulation in mESC


title: RNA-seq of Pax6 upregulation in mouse ESC_R1


title: co.Huh7+HCV_but_uninfected_GFP-_rep1

description:
co.Huh7+HCV_but_uninfected_GFP-_rep1
Counts_Huh7.txt

value: cultured cells


title: mESC Sm Expt. 1 - Sample 05

source_name: mESC

value: mESC

value: F121-9 mESC line (RRID:CVCL_VC42)


title: ChIP-seq of Pax6 in Zfp608 promoter deletion NPC_R1


title: ChIP-seq of Pol2 in Zfp608 promoter deletion NPC_R2


title: RNA-seq of element A and B deletion in mouse ESC_R2

value: mESC dAB

value: double deletion of elements A and B


title: co.Huh7+HCV_infected_GFP+_rep1

description:
co.Huh7+HCV_infected_GFP+_rep1
Counts_Huh7.txt

value: hepatocyte-derived cancer cell line


title: RNA-seq of element A and B deletion in mouse ESC_R1


title: ChIP-seq of Pol2 in Zfp608 promoter deletion NPC_R1

value: E14tg2a differentiated into neuronal progenitor cells (NPCs)


title: RNA-seq of element B deletion in mouse ESC_R2

value: mESC dB

value: deletion of element B


title: mESC Sm Expt. 1 - Sample 03


title: ChIP-seq of Rad21 in Zfp608 promoter deletion NPC_R2


title: mESC Sm Expt. 1 - Sample 04


title: Zygote Sl Expt. 1 - Sample 02

value: Zygote


title: RNA-seq of element B deletion in mouse ESC_R1


title: mESC Sm Expt. 1 - Sample 02


title: Huh7+HCV_but_uninfected_GFP-_rep1

description:
Huh7+HCV_but_uninfected_GFP-_rep1
Counts_Huh7.txt


title: Zygote Sl Expt. 1 - Sample 01


title: RNA-seq of element A deletion in mouse ESC_R2

value: mESC dA

value: deletion of element A


title: ChIP-seq of Rad21 in Zfp608 promoter deletion NPC_R1

value: NPC dprom

value: deletion Zfp608 promoter


title: mESC Sm Expt. 1 - Sample 01


title: ChIP-seq of CTCF in Zfp608 promoter deletion NPC_R2


title: RNA-seq of element A deletion in mouse ESC_R1


title: mESC Se Expt. 1 - Sample 05


title: Huh7+HCV_infected_GFP+_rep2

description:
Huh7+HCV_infected_GFP+_rep2
Counts_Huh7.txt


title: iMac+HCV_rep2

description:
iMac+HCV_rep2
Counts_Huh7.txt

value: human embryonic stem cell line H1-derived macropahge-like cells


title: RNA-seq of polyA insertion at Zfp608 in mouse ESC_R2

value: mESC polyA

value: polyA insertion at Zfp608 TSS


title: ChIP-seq of CTCF in Zfp608 promoter deletion NPC_R1


title: mESC Se Expt. 1 - Sample 04


title: iMac+HCV_rep1

description:
iMac+HCV_rep1
Counts_Huh7.txt

value: cultured cells


title: RNA-seq of polyA insertion at Zfp608 in mouse ESC_R1


title: ChIP-seq of H3K36me3 in Zfp608 promoter deletion NPC_R2


title: mESC Se Expt. 1 - Sample 03

value: mESC


title: RNA-seq of Zfp608 promoter deletion in  mouse ESC_R2

value: mESC dprom


title: mESC Se Expt. 1 - Sample 02

value: F121-9 mESC line (RRID:CVCL_VC42)


title: Huh7+HCV_but_uninfected_GFP-_rep2

description:
Huh7+HCV_but_uninfected_GFP-_rep2
Counts_Huh7.txt


title: co.D5.iMac_rep2

description:
co.D5.iMac_rep2
Counts_pHH.txt


title: ChIP-seq of H3K36me3 in Zfp608 promoter deletion NPC_R1


title: co.D5.iMac_rep1

description:
co.D5.iMac_rep1
Counts_pHH.txt


title: mESC Se Expt. 1 - Sample 01


title: ChIP-seq of H3K27Ac in Zfp608 promoter deletion NPC_R2


title: ChIP-seq of H3K27Ac in Zfp608 promoter deletion NPC_R1


title: mESC G1 Expt. 1 - Sample 06


title: RNA-seq of Zfp608 promoter deletion in  mouse ESC_R1


title: co.D5.pHH_rep2

description:
co.D5.pHH_rep2
Counts_pHH.txt

source_name: primary cells

value: primary cells

value: primary human hepatocytes


title: co.D5.pHH_rep1

description:
co.D5.pHH_rep1
Counts_pHH.txt


title: Huh7+HCV_infected_GFP+_rep1

description:
Huh7+HCV_infected_GFP+_rep1
Counts_Huh7.txt

value: hepatocyte-derived cancer cell line


title: RNA-seq of wt mouse ESC_R2

value: mESC wt

value: Wild type


title: ChIP-seq of H3K4me3 in Zfp608 promoter deletion NPC_R2

value: E14tg2a differentiated into neuronal progenitor cells (NPCs)


title: RNA-seq of wt mouse ESC_R1


title: mESC G1 Expt. 1 - Sample 05


title: ChIP-seq of H3K4me3 in Zfp608 promoter deletion NPC_R1


title: transwell.D3.iMac_rep2

description:
transwell.D3.iMac_rep2
Counts_pHH.txt


title: transwell.D3.iMac_rep1

description:
transwell.D3.iMac_rep1
Counts_pHH.txt


title: ChIP-seq INPUT in Zfp608 promoter deletion ESC


title: N5

first: Wenchang

last: Zhou

address: 180# Feng-Lin Road, Shanghai, 200032, China

institute: Zhongshan Hospital, Fudan University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count and fpkm values for each Sample

source_name: CD8+ T cell

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: agent

value: 10mM NAC

value: CD8+ T cell

value: WT


title: N4


title: mESC G1 Expt. 1 - Sample 03


title: transwell.D3.pHH_rep2

description:
transwell.D3.pHH_rep2
Counts_pHH.txt


title: ChIP-seq of Pol2 in Zfp608 promoter deletion ESC_R2

value: deletion Zfp608 promoter


title: mESC G1 Expt. 1 - Sample 04


title: N3


title: ChIP-seq of Pol2 in Zfp608 promoter deletion ESC_R1


title: transwell.D3.pHH_rep1

description:
transwell.D3.pHH_rep1
Counts_pHH.txt


title: N2


title: ChIP-seq of Rad21 in Zfp608 promoter deletion ESC_R2


title: 2C Mid S Expt. 2 - Sample C7

source_name: 2-Cell Embryo

value: 2-Cell Embryo

value: Nocodazole synchronization


title: 2C Mid S Expt. 2 - Sample C6


title: co.D3.iMac_rep2

description:
co.D3.iMac_rep2
Counts_pHH.txt

value: human embryonic stem cell line H1-derived macropahge-like cells


title: N1


title: ChIP-seq of Rad21 in Zfp608 promoter deletion ESC_R1


title: co.D3.iMac_rep1

description:
co.D3.iMac_rep1
Counts_pHH.txt

value: cultured cells


title: 2C Mid S Expt. 2 - Sample C5


title: 2C Mid S Expt. 2 - Sample C4


title: ChIP-seq of CTCF in Zfp608 promoter deletion ESC_R2


title: co.D3.pHH_rep2

description:
co.D3.pHH_rep2
Counts_pHH.txt


title: 2C Mid S Expt. 2 - Sample C3


title: ChIP-seq of CTCF in Zfp608 promoter deletion ESC_R1


title: C4


title: 2C Mid S Expt. 2 - Sample C2


title: ChIP-seq of H3K36me3 in Zfp608 promoter deletion ESC_R2


title: pHH.Ctrl_rep2

description:
pHH.Ctrl_rep2
Counts_pHH.txt


title: pHH.Ctrl_rep1

description:
pHH.Ctrl_rep1
Counts_pHH.txt


title: C2


title: 2C Late S Expt. 2 - Sample D8


title: iMAC.Ctrl_for_pHH_rep2

description:
iMAC.Ctrl_for_pHH_rep2
Counts_pHH.txt


title: C1


title: 2C Mid S Expt. 2 - Sample C1


title: ChIP-seq of H3K27Ac in Zfp608 promoter deletion ESC_R2


title: 2C Late S Expt. 2 - Sample D7


title: ChIP-seq of H3K27Ac in Zfp608 promoter deletion ESC_R1


title: 2C Late S Expt. 2 - Sample D6


title: ChIP-seq of H3K4me3 in Zfp608 promoter deletion ESC_R2


title: bCat_E18_1

city: Prague

first: Mehmet

middle: Mahsum

last: Kaplan

address: Vídeňská 1083

department: Department of Developmental Biology

country: Czech Republic

institute: Czech Academy of Sciences

description: FFPE Spatial Transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FAST files
Sequences were aligned to mm10 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseg coding genes were quantified using Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: barcodes.tsv.oz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.qz: gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz hi-res image of tissue
Supplementary files format and content: tissue lowes image.png.gz: low-res image of tissue
Supplementary files format and content: tissue positions list.csv.qz: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: web_summary.html: 10X websummary of captured RNAs accross the tissue and QC metrics
Supplementary files format and content: spatial_enrichment.cvs: spatial enrichment of features
Supplementary files format and content: .Rds: Single seurat objects loaded to R environment or mulltiple samples integrated

source_name: diaphragm E18.5

extract_protocol:
Formaldehyde fixed parafin embedded, 5µm diaphragm sections by a microtome.
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatail Gene Expression Slides & Reagent kit according to manufacturer's construction
OTHER: Spatial Transcriptomics

value: diaphragm E18.5

value: bCat cKO


title: dysgenic_E18_1

description: FFPE Spatial Transcriptome sequencing


title: iMac_day14_scRNA-seq

data_processing:
for scRNA-seq, raw data were input to cellrnager V3.1 pipeline, which performed cell demultiplexing, read mapping, UMI counting and cell filtering
for scATAC-seq, raw data were input to cellrnager-atac V1.1 pipeline, which performed cell demultiplexing, read mapping, peak calling and cell filtering
Assembly: GRCh38
Supplementary files format and content: for scRNA-seq, matrix files generated by cellranger pipeline
Supplementary files format and content: for scATAC-seq, ATAC fragments generated by cellranger-ATAC format

growth_protocol: Undifferentiated hESCs was cultured in E8 medium. Macrophage differenitiation was performed according to Duan et al Stem Cell Research and Therapy 2018 (10.1186/s13287-018-0934-x), HSPC was collected, macrophage differentiation was induced with medium supplemented with 50 ng/mL  M-CSF and 10 ng/mL IL-3 (Novoprotein) for 6 days and cells were collected for single cell analysis.

extract_protocol:
Differentiated cells on day 14 were dissociated with Accutase and filtered through a 70um cell strainer to obtain a single-cell suspension. Cells were spun down at 4 °C 300 g for 3 min and resuspended with FACS buffer to a final concentration of 2 million cells/mL. Live/dead assay showed around 85% of the cells were viable.
libraries were generated according to 10X genomics's instrument instructions.

treatment_protocol: On differentiation day 14, macrophage differentiation culture was used for scRNA-seq and scATAC-seq analysis.

value: Embryonic stem cells


title: 2C Late S Expt. 2 - Sample D4


title: 2C Late S Expt. 2 - Sample D5


title: co.D3.pHH_rep1

description:
co.D3.pHH_rep1
Counts_pHH.txt

value: primary cells


title: C3


title: iMac_day14_scATAC-seq

library_source: genomic single cell


title: FGFR4-28HTM-28z_CD276-8HTM-BBz_BiCisCAR_5_RNA

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

description: FGFR4-28HTM-28z_CD276-8HTM-BBz_BiCisCAR_5_raw_feature_bc_matrix.h5

data_processing:
CITE-seq including cell surfae protein and gene expression
fastq generation: Illumina bcl2fastq 2.20
sample demultiplexing: popscle demuxlet (https://github.com/statgen/popscle)
Alignment, CellRanger v7.0.1 (STAR 2.7.2a) (10x Genomics)
secondary analysis: Seurat 4.0.0 (R package)
Assembly: GRCh38-2020-A and CAR binder genome sequences
Supplementary files format and content: h5 file

source_name: Peripheral Blood Mononuclear Cells(PBMCs)

extract_protocol: 3E+06 of luciferase labeling JR cells (an aggressive RMS cells) were resuspended in Matrigel (Corning) after washing and intramuscularly injected into the NSG mice. 13 days later, 2.5E+06 FGFR4 or CD276 CAR T cells were intravenously injected into above tumor bearing NSG mice. Tumor infiltrating lymphocytes (TILs) from the RMS JR model were purified from tumors 11 days after T cell administration using 40% and 70% percoll (Cytiva, Cat# 17089102) gradient separation and then sorted viable human CD45+ lymphocytes on BD FACSAria Fusion and BD FACSAria UV. After washing with CITE-seq antibody staining buffer (DPBS with 0.05% BSA), sorted TILs were counted, resuspend at a concentration of 1E+06/50μL and stained with TotalSeq-C human “hashtag” antibodies (hashtag 5 or hashtag 6) for each mouse from 5 CAR T cells treated groups, allowing identification of different replicates from each group in the analysis. Next, above TILs were individually stained with a cocktail of a TotalSeq-C human lyophilized panel (BioLegend) of 17 surface proteins. After 3 washes, TILs were resuspended in PBS and counted and then replicates in each group were combined before proceeding immediately to single-cell immune profiling using a Chromium Single Cell 5’ Solution v2 platform system (10× Genomics). 10X Genomics 5’ single-cell gene expression and cell-surface protein tag libraries were prepared as instructed by the 10X Genomics user’s guides. Both libraries were sequenced on an Illumina NextSeq 500 individually.

value: PBMCs transduced with FGFR4-28HTM-28z_CD276-8HTM-BBz  BiCisCAR construct

value: CAR T- cells isolated from JR xenograft tumor 11 days post infusion

tag: fraction

value: mRNA


title: dysgenic_E14_1

description: FFPE Spatial Transcriptome sequencing

source_name: diaphragm E14.5

value: diaphragm E14.5


title: ChIP-seq of H3K36me3 in Zfp608 promoter deletion ESC_R1

value: mESC dprom


title: 2C Late S Expt. 2 - Sample D3


title: FGFR4-28HTM-28z_CD276-8HTM-BBz_BiCisCAR_5_CSP

data_processing:
CITE-seq including cell surfae protein and gene expression
fastq generation: Illumina bcl2fastq 2.20
sample demultiplexing: popscle demuxlet (https://github.com/statgen/popscle)
Alignment, CellRanger v7.0.1 (STAR 2.7.2a) (10x Genomics)
secondary analysis: Seurat 4.0.0 (R package)
Assembly: GRCh38-2020-A and CAR binder genome sequences
Supplementary files format and content: h5 file
Library strategy: CITE-seq

value: cell surface Protein (CSP)


title: 2C Late S Expt. 2 - Sample D2


title: ChIP-seq of Pax6 in wt NPC_R1

value: E14tg2a differentiated into neuronal progenitor cells (NPCs)

value: NPC wt

value: Wild type


title: ChIP-seq of Pax6 in wt NPC_R2


title: ChIP-seq of Pol2 in wt NPC_R1


title: 2C Late S Expt. 2 - Sample D1

value: 2-Cell Embryo


title: FGFR4-28HTM-BBz_CD276-8HTM-BBz_BiCisCAR_4_CSP

description: FGFR4-28HTM-BBz_CD276-8HTM-BBz_BiCisCAR_4_raw_feature_bc_matrix.h5

value: PBMCs transduced with FGFR4-28HTM-BBz_CD276-8HTM-BBz  BiCisCAR construct


title: control_E14_2

description: FFPE Spatial Transcriptome sequencing

value: control


title: control_E18_1

description: FFPE Spatial Transcriptome sequencing


title: iMAC.Ctrl_for_pHH_rep1

description:
iMAC.Ctrl_for_pHH_rep1
Counts_pHH.txt

value: cultured cells

value: human embryonic stem cell line H1-derived macropahge-like cells


title: 2C Early S Expt. 2 - Sample B7

value: Nocodazole synchronization


title: control_E14_3

description: FFPE Spatial Transcriptome sequencing


title: ChIP-seq of H3K4me3 in Zfp608 promoter deletion ESC_R1

value: deletion Zfp608 promoter


title: ChIP-seq of Pol2 in wt NPC_R2


title: control_E14_1

description: FFPE Spatial Transcriptome sequencing


title: control_E18_2

description: FFPE Spatial Transcriptome sequencing

value: diaphragm E18.5


title: ChIP-seq INPUT in wt NPC


title: CD276-8HTM-BBz_CAR_3_RNA

description: CD276-8HTM-BBz_CAR_3_raw_feature_bc_matrix.h5

value: PBMCs transduced with CD276-8HTM-BBz CAR construct


title: CD276-8HTM-BBz CAR_3_CSP

value: CAR T- cells isolated from JR xenograft tumor 11 days post infusion


title: CD8+ TIls, cKO SM

first: Guilai

last: Liu

state: Jiangsu

address: Longmian road 639

institute: China Pharmaceutical University

data_processing:
FastQC (v0.11.9) was applied for quality control.
Quality-filtered reads were then mapped to the reference genome using Bowtie (v2.2.5), and only uniquely mapped reads were kept.
Sam files were converted to Bam format using Samtools (v1.3.1).
MACS2 (v2.1.1.20160309) was used to call peaks with the sonicated input as a control and an initial threshold q-value of 0.01 as the cutoff.
Visualization of read count data was performed by converting raw bam files to bigwig files using IGV tools. Edge R was used to identify differential expressions and calculate the P values.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: subcutaneous MC38 tumors

extract_protocol:
Subcutaneous MC38 tumors were minced by razors, dissociated by using gentle MACS dissociator (Miltenyi Biotec) to single cell suspension, and passed through a 70 μm mesh nylon strainer, from which CD8+ TILs were sorted using the BD FACS ARIA II SORP (BD Biosciences) and resuspended in 1 mL PBS.
Cells were resuspended in the transposition reaction mixture (Nextera DNA Library Preparation Kit, Illumina) and incubated at 37℃ for 30 min. After transposition, DNA was immediately purified with the MinElute PCR purification kit (Qiagen). To amplify transposable DNA fragments, barcode PCR primers were used for PCR. Then the amplification library was purified with the MinElute PCR purification kit and sequenced by Illumina NovaSeq 6000 (75 bp; paired-end).

treatment_protocol: Acsl4-cKO Mice inoculed with subcutaneous MC38 tumors were treated with vehicle or SM, Acsl4f/f mice bearing subcutaneous MC38 tumors were treated with vehicle as control.

value: subcutaneous MC38 tumors

tag: animal age

value: T cell

value: SM


title: 2C Early S Expt. 2 - Sample B6


title: 2C Early S Expt. 2 - Sample B5


title: ChIP-seq of Rad21 in wt NPC_R1

data_processing:
Data were mapped using bowtie2, the duplicated reads were discarded and bigwigs were produced directly from deduplicated bam files. For detailed protocol see the methods section of the adjoining paper.
Assembly: mm10
Supplementary files format and content: Processed files are given as a bigwig file of the two merged replicates.


title: CD8+ TIls, cKO ctrl

value: vehicle


title: FGFR4-28HTM-28z_CAR_2_RNA

description: FGFR4-28HTM-28z_CAR_2_raw_feature_bc_matrix.h5

value: PBMCs transduced with FGFR4-28HTM-28z CAR construct

value: mRNA


title: ChIP-seq of Rad21 in wt NPC_R2

value: E14tg2a differentiated into neuronal progenitor cells (NPCs)

value: NPC wt

value: Wild type


title: ChIP-seq of CTCF in wt NPC_R1


title: 2C Early S Expt. 2 - Sample B4

value: 2-Cell Embryo


title: CD8+ TIls, WT ctrl


title: FGFR4-28HTM-28z_CAR_2_CSP

value: cell surface Protein (CSP)


title: 2C Early S Expt. 2 - Sample B3


title: FGFR4-28HTM-BBz_CAR_1-2_RNA

description: FGFR4-28HTM-BBz_CAR_1-2_raw_feature_bc_matrix.h5

value: PBMCs transduced with FGFR4-28HTM-BBz CAR construct


title: FGFR4-28HTM-BBz_CD276-8HTM-BBz_BiCisCAR_4_RNA

value: PBMCs transduced with FGFR4-28HTM-BBz_CD276-8HTM-BBz  BiCisCAR construct


title: ChIP-seq of H3K36me3 in wt NPC_R1


title: FGFR4-28HTM-BBz_CAR_1-2_CSP


title: 2C Early S Expt. 2 - Sample B1

value: Nocodazole synchronization


title: Heart Muscle, hRXFP1tg, 8 wk TAC surgery, rep8

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

data_processing:
trimmed with trim_galore version 0.6.4. Parameters: --length 26 --phred33
counts created with TopHat (-p 16 -g 1 --segment-length 25 -i 30 -I 3000) run (v2.1.1), bowtie 2.2.9
CPM values created with cpm from edgeR package 3.17
Assembly: mm10
Supplementary files format and content: raw counts created with TopHat
Supplementary files format and content: CPM values created with edgeR

source_name: Heart Muscle (LV)

extract_protocol:
RNA was harvested using the Trizol kit (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard BGISeq-500 protocols, strand specific mRNA sequencing on DNBSEQ platform PE100bp

value: Heart Muscle (LV)

value: TG

value: TAC


title: ChIP-seq of H3K36me3 in wt NPC_R2

extract_protocol:
Chromatin was fixed with 1% formaldehyde for 10 min at RT. Cells were lysed and IP done using Diagenone iDeal ChIP-seq kit for TFs or histones according to the manufacturer's recommendation.
Libraries were constructed by BGI


title: Heart Muscle, hRXFP1tg, 8 wk TAC surgery, rep9


title: Heart Muscle, hRXFP1tg, 8 wk TAC surgery, rep10


title: 2C G1 Expt. 2 - Sample A4


title: Heart Muscle, hRXFP1tg, 8 wk TAC surgery, rep7


title: ChIP-seq of H3K27Ac in wt NPC_R1


title: FGFR4-28HTM-BBz_CAR_1-1_CSP

description: FGFR4-28HTM-BBz_CAR_1-1_raw_feature_bc_matrix.h5

value: CAR T- cells isolated from JR xenograft tumor 11 days post infusion


title: 2C G1 Expt. 2 - Sample A3


title: Heart Muscle, hRXFP1tg, 8 wk TAC surgery, rep6


title: Heart Muscle, hRXFP1tg, 8 wk TAC surgery, rep5


title: C5

value: CD8+ T cell

value: WT


title: RNA-seq data for sample tumor T447

city: paris

first: Elodie

last: chapeaublanc

address: 26 rue d'ulm

department: UMR 144

institute: Institut Curie

data_processing:
Protocol : Nugen Ovation Solo
NovaSeq - S1 - PE100
aligner : STAR
Data were integrated using Deseq2 default parameters and VST normalisation.
Genome_build: human hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text files include Deseq2 values for all samples (sample as column)

extract_protocol:
Tumours RNA were extracted using Triple extraction protocol
The pool of libraries was quantified using a qPCR method (KAPA library quantification kit, Roche). The sequencing was carried out using paired-end mode (PE100) on a Illumina Novaseq 6000 instrument, using a custom primer (provided into the Nugen kit) to initiate the Read 1 sequencing. The target number of reads was about 50 million paired-reads per sample.

value: Bladder carcinoma tumor

tag: tumor name in article

tag: Stage

value: MIBC

tag: mibc consensus classification (rnaseq)

value: Ba/Sq


title: RNA-seq data for sample tumor T3395

value: LumNS


title: ChIP-seq of H3K4me3 in wt NPC_R2

value: E14tg2a differentiated into neuronal progenitor cells (NPCs)

value: NPC wt


title: 2C G1 Expt. 2- Sample A1

value: 2-Cell Embryo


title: Heart Muscle, hRXFP1tg, 8 wk TAC surgery, rep4


title: ChIP-seq of CTCF in wt NPC_R2

value: Wild type


title: 2C Early S Expt. 2 - Sample B2


title: 2C Mid S Expt. 1 - Sample C6


title: ChIP-seq INPUT in wt ESC

value: mESC wt


title: RNA-seq data for sample tumor T391


title: FGFR4-28HTM-BBz_CAR_1-1_RNA

value: PBMCs transduced with FGFR4-28HTM-BBz CAR construct

value: mRNA


title: RNA-seq data for sample tumor T1087_1

value: LumP


title: 2C Mid S Expt. 1  - Sample C5

value: Nocodazole synchronization


title: RNA-seq data for sample tumor T924_1


title: Heart Muscle, hRXFP1tg, 8 wk TAC surgery, rep2

value: Heart Muscle (LV)

value: TG

value: TAC


title: ChIP-seq of Pol2 in wt ESC_R2


title: ChIP-seq of Pol2 in wt ESC_R1


title: ChIP-seq of H3K27Ac in wt NPC_R2


title: Heart Muscle, hRXFP1tg, 8 wk TAC surgery, rep1


title: 2C G1 Expt. 2 - Sample A2


title: RNA-seq data for sample tumor T1033

value: Stroma-rich


title: ChIP-seq of Rad21 in wt ESC_R2


title: Heart Muscle, hRXFP1tg, Sham, rep5

value: Sham


title: ChIP-seq of H3K4me3 in wt NPC_R1


title: 2C Mid S Expt. 1 - Sample C4


title: 2C Mid S Expt. 1 - Sample C3


title: RNA-seq data for sample tumor T791_2

value: Bladder carcinoma tumor

value: NMIBC


title: Heart Muscle, hRXFP1tg, Sham, rep4


title: 2C Mid S Expt. 1 - Sample C2


title: ChIP-seq of Rad21 in wt ESC_R1


title: RNA-seq data for sample tumor T1025


title: 2C Mid S Expt. 1 - Sample C1


title: ChIP-seq of CTCF in wt ESC_R2


title: RNA-seq data for sample tumor T813_1

value: MIBC


title: Heart Muscle, hRXFP1tg, Sham, rep3


title: Heart Muscle, hRXFP1tg, 8 wk TAC surgery, rep3


title: ChIP-seq of CTCF in wt ESC_R1


title: RNA-seq data for sample tumor T1156

value: Ba/Sq


title: 2C Late S Expt. 1 - Sample D5


title: 2C Late S Expt. 1 - Sample D4


title: ChIP-seq of H3K36me3 in wt ESC_R2


title: Heart Muscle, Wildtype, 8 wk TAC surgery, rep10

value: NTG


title: ChIP-seq of H3K36me3 in wt ESC_R1


title: RNA-seq data for sample tumor T1211_2


title: 2C Late S Expt. 1 - Sample D3

value: 2-Cell Embryo


title: Heart Muscle, Wildtype, 8 wk TAC surgery, rep9


title: 2C Late S Expt. 1 - Sample D2


title: RNA-seq data for sample tumor T1175

value: LumU


title: ChIP-seq of H3K27Ac in wt ESC_R2

value: mESC wt

value: Wild type


title: 2C Late S Expt. 1 - Sample D1


title: RNA-seq data for sample tumor T877

value: LumNS


title: ChIP-seq of H3K4me3 in wt ESC_R2


title: Heart Muscle, Wildtype, 8 wk TAC surgery, rep7


title: RNA-seq data for sample tumor T839


title: RNA-seq data for sample tumor T2542


title: 2C Early S Expt. 1 - Sample B3


title: 2C Early S Expt. 1 - Sample B4


title: ChIP-seq of H3K4me3 in wt ESC_R1


title: Heart Muscle, Wildtype, 8 wk TAC surgery, rep5


title: Mtb, Ab-SigA, ChIP-seq, replicate 3

city: Newyork

first: Shixin

address: 1230 York AV

institute: The Rockefeller University

data_processing:
Basecalls performed using bcl2fastq ver 2.16 for NextSeq paired reads.
ChIP-seq reads were trimmed with Cutadapt v4.3 to remove low quailty parts (<30) and short reads (<18 bp)
ChIP-seq reads were aligned to the Mtb H37RV genome using Bowtie2 V2.5.1. Only paired and uniquely mapping reads with at most 1 mismatch were retained.
The ChIP-seq coverage were generated by extending each pair of reads to represent sequenced framents.
The ChIP-seq coverage were applied to downstream analysis with custom scripts.
Assembly: Mycobacterium tuberculosis H37RV, NC_018143.2
Supplementary files format and content: wig files for ChIP signal

organism: Mycobacterium tuberculosis

source_name: bacterial cell

growth_protocol: Mycobacterium tuberculosis (Mtb) H37Rv was grown at 37 °C in a minimal medium (Difco Middlebrook 7H9 broth) supplemented with 0.5% (v/v) glycerol, 0.05% (v/v) tyloxapol, 0.2 g L-1 casamino acids, 0.024 g L-1 pantothenic acid and 10% (v/v) OADC (BD). The double auxotrophic Mtb mc2 6206 strain (H37Rv ΔpanCD ΔleuCD)21 was grown in minimal medium with an additional 50 mg L-1 L-leucine (Sigma) and 24 mg mL-1  pantothenic acid (Sigma).

extract_protocol:
Mtb cells were treated with 1% formaldehyde for 30 min and the crosslinking was quenched by adding glycine to a final concentration of 250 mM for another 30 min. After bead-beating, the supernatant was treated with MNase for 15 min in a 37 °C incubator.
The sequencing libraries for immunoprecipitated DNA and input control were prepared using the NEBNext Ultra II DNA Library Prep Kit. Libraries were amplified 11 cycles on the thermocycler.

treatment_protocol: The cells were treated with 50 µg/ml rifampicin or equal volume of DMSO if needed.

value: bacterial cell

tag: chip antibody

value: Anti-Eco s70 antibody (BioLegend, 663208)


title: Heart Muscle, hRXFP1tg, Sham, rep2

value: Heart Muscle (LV)


title: Heart Muscle, Wildtype, 8 wk TAC surgery, rep8


title: Mtb, Ab-SigA, ChIP-seq, replicate 2


title: Heart Muscle, Wildtype, 8 wk TAC surgery, rep4


title: Heart Muscle, hRXFP1tg, Sham, rep1

value: TG


title: 2C Early S Expt. 1 - Sample B1

value: Nocodazole synchronization


title: cHiC of CTCF motif deletion at element A in mouse NPC at the Zfp608 locus_R1

first: Ivana

address: 141 rue de la Cardonille

institute: IGH, CNRS

data_processing:
Hi-C data was processed using the TADbit tool (https://github.com/3DGenomes/tadbit). In brief, raw sequencing reads were mapped independently to the reference genome using Bowtie2 in local alignment mode and non-informative reads were removed using the default options. See adjoning paper for the detailed pipeline.
Assembly: mm10
Supplementary files format and content: Each processed file represent pairwise information of the observed genome contacts. For score files: the data was analyzed with "misha" (https://github.com/tanaylab/misha) database entry and scores were generated using the "shaman" pipeline (https://github.com/tanaylab/shaman). The .mcool files were produced using the cooler package (https://cooler.readthedocs.io/en/latest/index.html).

extract_protocol:
Cell lysis, digestion, ligation, sonication and biotin labeling was preformed as in in-situ Hi-C protocol from Rao et al 2014. The rest of the protocol was done with SureSelect Agilent capture kit and custom capture library. For detailed protocol see adjoning paper.
Libraries were prepared with the SureSelect Agilent kit. For detailed protocol see adjoning paper.
cHi-C

tag: cell line

value: E14tg2a differentiated into neuronal progenitor cells (NPCs)

value: NPC dCTCF

value: deletion of CTCF motif at element A


title: Mtb, Ab-SigA, ChIP-seq, replicate 1

tag: cell type


title: ChIP-seq of H3K27Ac in wt ESC_R1


title: 2C G1 Expt. 1 - Sample A3

tag: tissue


title: cHiC of element A and B deletion in mouse NPC at the Zfp608 locus_R2

value: NPC dAB

value: double deletion of elements A and B


title: Heart Muscle, Wildtype, 8 wk TAC surgery, rep3

value: TAC


title: Heart Muscle, Wildtype, 8 wk TAC surgery, rep2

value: NTG


title: Mtb, Rifampicin 30 min, Ab-RpoB, ChIP-seq, replicate 2

value: Rifampicin 30 min

value: anti-Eco RNAP beta antibody (BioLegend, 663903)


title: cHiC of element A and B deletion in mouse NPC at the Zfp608 locus_R1


title: cHiC of element B deletion in mouse NPC at the Zfp608 locus_R2

value: NPC dB

value: deletion of element B


title: Heart Muscle, Wildtype, 8 wk TAC surgery, rep1


title: 2C G1 Expt. 1- Sample A1

value: 2-Cell Embryo


title: Mtb, Rifampicin 30 min, Ab-RpoB, ChIP-seq, replicate 1

value: bacterial cell


title: Mtb, DMSO 30 min, Ab-RpoB, ChIP-seq, replicate 2

value: DMSO 30 min


title: Heart Muscle, Wildtype, 8 wk TAC surgery, rep6

value: Heart Muscle (LV)


title: 2C Early S Expt. 1 - Sample B2


title: Heart Muscle, Wildtype, Sham, rep5

value: Sham


title: cHiC of element B deletion in mouse NPC at the Zfp608 locus_R1


title: cHiC of CTCF motif deletion at element A in mouse NPC at the Zfp608 locus_R2


title: Bladder tissue biopsy from healthy donor 2

first: Fei

last: Su

state: Shanghai

address: 800 Dongchuan Road

department: School of Life Science and Biotechnology

institute: Shanghai Jiao Tong University

data_processing:
Basecalls performed using CASAVA
Data analysis was performed with CellRanger 3.0
Genome_build: Hg38
Supplementary_files_format_and_content: mtx files were generated from CellRanger
Supplementary_files_format_and_content: tsv files were generated from CellRanger

source_name: Bladder tissue

extract_protocol: Single-cell suspensions were converted to barcoded scRNA-seq libraries by using the Chromium Single Cell 3’ Library, Gel Bead & Multiplex Kit, and Chip Kit (10X Genomics), aiming for an estimated 10,000 cells per library. Samples were processed using kits pertaining to V3 barcoding chemistry of 10X Genomics.

treatment_protocol: No treatment was performed

value: Bladder

tag: disease state

value: Healthy donor

tag: group

value: Healthy Control


title: Mtb, DMSO 30 min, Ab-RpoB, ChIP-seq, replicate 1

tag: treatment


title: Bladder tissue biopsy from healthy donor 1


title: Heart Muscle, Wildtype, Sham, rep4

tag: genotype


title: Mtb, Rifampicin 30min, input DNA

tag: strain

value: Rifampicin 30min


title: cHiC of element A deletion in mouse NPC at the Zfp608 locus_R2

value: E14tg2a differentiated into neuronal progenitor cells (NPCs)

value: NPC dA

value: deletion of element A


title: Heart Muscle, Wildtype, Sham, rep3

value: NTG


title: Bladder tissue biopsy from IC/BPS patient 4

value: Interstitial cystitis/bladder pain syndrome without Hunner lesions

value: NHIC


title: Mtb, Ab-RpoB, ChIP-seq, replicate 2

value: anti-Eco RNAP beta antibody (BioLegend, 663903)


title: Mtb, Ab-RpoB, ChIP-seq, replicate 1


title: cHiC of element A deletion in mouse NPC at the Zfp608 locus_R1


title: Mtb, DMSO 30min, input DNA

value: DMSO 30min


title: cHiC of Zfp608 promoter deletion in  mouse NPC at the Zfp608 locus_R2

value: NPC dprom

value: deletion Zfp608 promoter


title: 2C G1 Expt. 1 - Sample A2

data_processing:
Raw sequencing reads were trimmed, aligned and processed according to Miura et al., 2020 (PMID: 33230331).
Data processing of trimmed abd aligned reads were processed to obtain log2 fold replication timing values according to the methodology described by Miura et al. in their publication from 2020 (PMID: 33230331).
Assembly: mm10
Supplementary files format and content: BedGraph

value: 2-Cell Embryo

value: Nocodazole synchronization


title: cHiC of polyA insertion at Zfp608 in mouse NPC at the Zfp608 locus_R2

value: NPC polyA

value: polyA insertion at Zfp608 TSS


title: Bladder tissue biopsy from IC/BPS patient 2

value: Bladder

value: Interstitial cystitis/bladder pain syndrome with Hunner lesions

value: HIC


title: Yeast RNA, 218-L-14-D1690 (sup35-218), rep3

city: St. Petersburg

first: Yury

last: Barbitoff

address: Kantemirovskaya st. 2A

country: Russia

institute: Bioinformatics Institute

data_processing:
Raw RNA-seq reads were trimmed using Trimmomatic (Bolger et al., 2014; 10.1093/bioinformatics/btu170), keeping the first 100 bp of each read (the step was performed to ensure compatibility with earlier datasets obtained in the group)
Per-processed RNA-seq reads were aligned onto the yeast reference genome (Saccharomyces Genome Database R64-3-1) using Hisat2 (Kim et al., 2019; 10.1038/s41587-019-0201-4).
Quantification of gene expression was performed using featurecounts (Liao et al., 2014; 10.1093/bioinformatics/btt656) using yeast gene annotation obtained from Saccharomyces Genome Database (R64-3-1 version).
Assembly: Saccharomyces Genome Database S288C reference R64-3-1 (http://sgd-archive.yeastgenome.org/sequence/S288C_reference/genome_releases/S288C_reference_genome_R64-3-1_20210421.tgz)
Supplementary files format and content: A matrix table containing raw read counts for all genes in all samples.  Gene ID, chromosomal location, strand, and gene length are provided for each gene besides read counts.

organism: Saccharomyces cerevisiae

growth_protocol: For extraction of RNA, yeast cultures were grown in 30 ml of SC liquid medium until OD600 ~ 0.8–1.0. The cells were then harvested by centrifugation at 8000g for 5 minutes and washed.

extract_protocol:
Total yeast RNA was isolated using the GeneJET RNA Purification Kit #K0731 (Thermo Scientific, USA) according to the manufacturer's instructions. RNA concentration and quality were evaluated using a NanoDrop Spectrophotometer (Thermo Scientific, USA).
Preparation of libraries for sequencing was carried out using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB #E7765, MA, USA) and NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs Set 2) (NEB #E6442S, MA, USA).


title: cHiC of polyA insertion at Zfp608 in mouse NPC at the Zfp608 locus_R1

value: E14tg2a differentiated into neuronal progenitor cells (NPCs)


title: GBM39, HSR, RiboZero, rep1

city: Stanford

first: Guiping

last: Wang

address: 256 Campus Dr

institute: Stanford University

description:
GBM39HSR_RiboZero_rep1
Ribo-Zero RNA seq

data_processing:
Paired end reads were mapped to human reference genome (hg38) and gencode v42 using STAR, version 2.7.10b17, with --runMode alignReads
Reads with MAPQ values less than 10 were filtered using samtools 1.8
PCR duplicates are removed with Picard MarkDuplicates
Bigwig (.bw) files were generated for each strand using bamCoverage (py-deeptools/3.3.1_py36) with -binSize 10 --normalizeUsing CPM
Assembly: hg38
Supplementary files format and content: Bigwig (.bw) files contain normalized GRO-seq signal separated by DNA strands for visualization.

growth_protocol: COLO320 cells were grown in 4.5 g/L glucose formulated Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% FBS and 1% pen/strep. GBM39 cells were grown in DMEM/F12 supplemented with 1 x B27 , 20 ng/ml EGF, 20 ng/ml FGF, 5ug/ml Heparin and 1% pen/strep

extract_protocol:
Total RNA from each sample was isolated with Quick-RNA Miniprep Kit (Zymo Research, R1054) with input of 1-2 million cells.
Illumina Ribo-Zero Plus rRNA Depletion Kit is used to construct the library.

value: glioblastoma


title: Heart Muscle, Wildtype, Sham, rep1

value: Heart Muscle (LV)

value: Sham


title: Mtb, input DNA, replicate 1

value: bacterial cell


title: Yeast RNA, 218-L-14-D1690 (sup35-218), rep2


title: GBM39, HSR, RiboZero, rep2

description:
GBM39HSR_RiboZero_rep2
Ribo-Zero RNA seq


title: Bladder tissue biopsy from IC/BPS patient 5

value: Interstitial cystitis/bladder pain syndrome without Hunner lesions

value: NHIC


title: Bladder tissue biopsy from IC/BPS patient 1


title: cHiC of wt mouse NPC at the Zfp608 locus_R2

last: Jerkovic

value: NPC wt

value: Wild type


title: cHiC of Zfp608 promoter deletion in  mouse NPC at the Zfp608 locus_R1

value: NPC dprom

value: deletion Zfp608 promoter


title: Yeast RNA, 218-L-14-D1690 (sup35-218), rep1


title: SEnd-seq of total RNA 12h post rpoc-his induction, replicate 2

data_processing:
Basecalls performed using bcl2fastq ver 2.16 for NextSeq paired reads.
Paired-end reads were merged to single end fasta reads by usin FlASh software v1.2.11
Labled transcript 5' end and 3' end were extracted from merged single end reads and processed to paired-end reads again by custom program scripts
Extracted paired-end reads were mapped to Mtb(NC_018143.2 ) by using Bowtie2 v2.5.1, and single end full length sequence was generated by  the paried-end data by custome transcripts and Bowtie2.
rRNA transcripts were removed and TSSs, TTSs and overlap TTSs were extracted from the remaining data.
Assembly: Mycobacterium tuberculosis H37RV, NC_018143.2
Supplementary files format and content: wig files for RNA coverage
Library strategy: SEnd-seq

growth_protocol: Mycobacterium tuberculosis (Mtb) H37Rv was grown at 37 °C in a minimal medium (Difco Middlebrook 7H9 broth) supplemented with 0.5% (v/v) glycerol, 0.05% (v/v) tyloxapol, 0.2 g L-1 casamino acids, 0.024 g L-1 pantothenic acid and 10% (v/v) OADC (BD). The double auxotrophic Mtb mc2 6206 strain (H37Rv ΔpanCD ΔleuCD)21 was grown in minimal medium with an additional 50 mg L-1 L-leucine (Sigma) and 24 mg mL-1  pantothenic acid (Sigma). 100 ng mL-1 of ATc was added to induce the sgRNA or gene expression if needed.

extract_protocol:
Bacterial cells were quenched by adding 1x vol of GTC buffer (600 g L-1 guanidium thiocyanate, 5 g L-1 N-laurylsarcosine and 7.1 g L-1 sodium citrate and 0.7% (v/v) 2-mercaptoethanol) to the culture medium immediately before the harvest and placed it at room temperature for 15 min. Cell pellets were collected by centrifugation (4,000 g for 10 min at 4 °C), then thoroughly resuspended in 100 μl of TE buffer (10 mM Tris-HCl and 1 mM EDTA, pH8.0). After adding 1 ml of TRIzol Reagent (Invitrogen, 15596) and 300 mg of glass beads (Sigma,  G1145), the cells were immediately lysed by bead beating with the Precellys Evolution homogenizer at the highest speed 10,000 rpm for 4x 45s cycles with interval of 60s at 4°C. Then the RNA was extracted following TRIzol RNA purification protocol.
SEnd-seq strategy was used to prepare the SEnd-seq library

treatment_protocol: The cells were treated with 100 ng/ml ATc, 50 µg/ml rifampicin, 30 µg/ml of linezolid or equal volume of DMSO if needed.

value: Atc inducible rpoC-his

value: Atc

value: total RNA


title: Yeast RNA, L-14-D1690 (SUP35wt), rep3

value: MATa ade1-14(UGA) trp1-289(UAG) his3-d200 lys2 ura3-52 leu2-3,112 SUP35::HIS3MX [pRSU2]


title: Heart Muscle, Wildtype, Sham, rep2

value: NTG


title: cHiC of Pax6 upregulation in mouse ESC at the Zfp608 locus_R2

value: mESC upPAX6

value: Pax6 upregulation in mESC


title: Yeast RNA, L-14-D1690 (SUP35wt), rep4


title: cHiC of wt mouse NPC at the Zfp608 locus_R1

value: E14tg2a differentiated into neuronal progenitor cells (NPCs)


title: GBM39, ec, RiboZero, rep2

description:
GBM39ec_RiboZero_rep2
Ribo-Zero RNA seq

value: glioblastoma


title: SEnd-seq of total RNA 12h post rpoc-his induction, replicate 1


title: Yeast RNA, L-14-D1690 (SUP35wt), rep2


title: Mtb, input DNA, replicate 2


title: cHiC of Pax6 upregulation in mouse ESC at the Zfp608 locus_R1


title: GBM39, ec, RiboZero, rep1

description:
GBM39ec_RiboZero_rep1
Ribo-Zero RNA seq


title: COLO320, HSR, RiboZero, rep2

description:
COLO320HSR_RiboZero_rep2
Ribo-Zero RNA seq

value: colorectal carcinoma


title: Yeast RNA, L-14-D1690 (SUP35wt), rep1


title: SEnd-seq of total RNA without rpoc-his induction, replicate 1

value: bacterial cell

value: MeOH


title: SEnd_seq of total RNA from Mtb cells  upon  rho  knockdown 96 h and 20 min linezolid treatment, replicate 2

value: ATc inducible rho kd

value: ATc +Linezolid


title: COLO320, HSR, RiboZero, rep1

description:
COLO320HSR_RiboZero_rep1
Ribo-Zero RNA seq


title: cHiC of CTCF motif deletion at element A in mouse ESC at the Zfp608 locus_R1

value: mESC dCTCF

value: deletion of CTCF motif at element A


title: Yeast RNA, U-14-D1690 (SUP35wt), rep3


title: SEnd_seq of total RNA from Mtb cells  upon  rho  knockdown 96 h and 20 min linezolid treatment, replicate 1


title: cHiC of element A and B deletion in mouse ESC at the Zfp608 locus_R2

value: mESC dAB

value: double deletion of elements A and B


title: Yeast RNA, U-14-D1690 (SUP35wt), rep1


title: COLO320, HSR, TPL, input, rep2

data_processing:
*library strategy: Kethoxal-assisted single-stranded DNA sequencing (KAS-seq)
The sequence data were mapped to the hg38 assembly of the human genome using Bowtie19,20 with the following settings: -v 2-k 2-m 1--best--strata-X 1000.
Duplicate reads were removed using picard-tools (version 1.99).
MACS221 (v.2.1.1) was used for peak-calling with the following parameters: --broad -g hs --broad-cutoff 0.01 -q 0.01.
macs2 peaks were filtered to within ecDNA intervals.
Assembly: hg38
Supplementary files format and content: Bigwig (.bw) files containing normalized KAS-seq signal to input were generated for visualization.

growth_protocol: 4.5 g/L glucose formulated Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% FBS and 1% pen/strep.

extract_protocol:
Genomic DNA was then extracted using the Monarch gDNA Purification Kit (NEB T3010S) following the standard protocol but with elution using 50 µL 25 mM K3BO3 at pH 7.0.
Click reaction was carried out by mixing 87.5 µL purified DNA, 2.5 µL 20 mM DBCO-PEG4-biotin (DMSO solution, Sigma 760749), and 10 µL 10× PBS in a final volume of 100 µL. The reaction was then incubated at 37◦C for 90 minutes. DNA was purified using AMPure XP beads by adding 50 µL beads 100 µL reaction, washing beads on a magnetic stand twice with 80% EtOH, and eluting in 130 µL 25mM K3BO3. Purified DNA was then sheared using a Covaris E220 instrument down to ∼200-400 bp size. Pulldown of biotin-labeled DNA was initiated by separating 10 µL of 10 mg/mL Dynabeads MyOne Streptavidin T1 beads (Life Technologies, 65602) on a magnetic stand, then washing with 180 µL of 1× TWB (Tween Washing Buffer; 5 mM Tris-HCl pH 7.5; 0.5 mM EDTA; 1 M NaCl; 0.05% Tween 20). Beads were then resuspended in 300 µL of 2× Binding Buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA; 2 M NaCl), sonicated DNA was added (diluted to a final volume of 300 µL if necessary), and beads were incubated for ≥15 minutes at room temperature on a rotator. Beads were separated on a magnetic stand and washed with 300 µL of 1× TWB and heated at 55◦C in a Thermomixer with shaking at 1,000 rpm for 2 minutes. The supernatant was removed on a magnetic stand, and the TWB wash and 55◦C incubation were repeated.   Libraries were prepared on beads using the NEBNext Ultra II DNA Library Prep Kit (NEB, #E7645).

treatment_protocol: cell culture media was supplemented with 5 mM N3-kethoxal , and cells were incubated for 10 minutes at 37◦C in a 6-well plate.

value: 1uM triptolide for 3hr


title: cHiC of CTCF motif deletion at element A in mouse ESC at the Zfp608 locus_R2


title: Yeast RNA, U-14-D1690 (SUP35wt), rep2


title: COLO320, DM, RiboZero, rep1

description:
COLO320DM_RiboZero_rep1
Ribo-Zero RNA seq


title: cHiC of element A and B deletion in mouse ESC at the Zfp608 locus_R1


title: COLO320, DM, RiboZero, rep2

description:
COLO320DM_RiboZero_rep2
Ribo-Zero RNA seq


title: SEnd_seq of total RNA from Mtb cells  upon  rho  knockdown 96 h and 20 min Rifampicin treatment, replicate 1

value: ATc +Rifampicin

value: total RNA


title: cHiC of element B deletion in mouse ESC at the Zfp608 locus_R2

value: mESC dB

value: deletion of element B